Running examples in 'cgdsr-Ex.R' failed
The error most likely occurred in:

> ### Name: cgdsr-setPlotErrorMsg
> ### Title: Set custom plot error message
> ### Aliases: cgdsr-setPlotErrorMsg setPlotErrorMsg setPlotErrorMsg.CGDS
> 
> ### ** Examples
> 
> # Create CGDS object
> mycgds = CGDS("http://www.cbioportal.org/")
> 
> getCancerStudies(mycgds)
                     cancer_study_id
1                      paac_jhu_2014
2                      laml_tcga_pub
3                          laml_tcga
4                      acyc_fmi_2014
5                      acyc_mda_2015
6                    acyc_mskcc_2013
7                   acyc_sanger_2013
8                    acbc_mskcc_2015
9                           acc_tcga
10             blca_mskcc_solit_2014
11             blca_mskcc_solit_2012
12      blca_plasmacytoid_mskcc_2016
13                          blca_bgi
14           blca_dfarber_mskcc_2014
15                     blca_tcga_pub
16                         blca_tcga
17                          lgg_tcga
18                     brca_metabric
19                        brca_bccrc
20                        brca_broad
21                       brca_sanger
22                 brca_tcga_pub2015
23                     brca_tcga_pub
24                         brca_tcga
25         brca_bccrc_xenograft_2014
26               cellline_ccle_broad
27                         cesc_tcga
28                    chol_nccs_2013
29                     chol_nus_2012
30                         chol_tcga
31                   lcll_broad_2013
32                    cll_iuopa_2015
33                 ccrcc_utokyo_2013
34                coadread_dfci_2016
35                coadread_genentech
36                 coadread_tcga_pub
37                     coadread_tcga
38                    coadread_mskcc
39                ctcl_columbia_2015
40                 cscc_dfarber_2015
41                   desm_broad_2015
42                   dlbc_broad_2012
43                        esca_broad
44                         esca_tcga
45                         escc_icgc
46                    escc_ucla_2014
47                   es_iocurie_2014
48                 gbc_shanghai_2014
49                   egc_tmucih_2015
50                    prad_cpcg_2017
51                  gbm_tcga_pub2013
52                      gbm_tcga_pub
53                          gbm_tcga
54                        hnsc_broad
55                          hnsc_jhu
56                     hnsc_tcga_pub
57                         hnsc_tcga
58               liad_inserm_fr_2014
59                   all_stjude_2013
60                   all_stjude_2015
61               panet_shanghai_2013
62                     chol_jhu_2013
63                     kich_tcga_pub
64                         kich_tcga
65                          kirc_bgi
66                     kirc_tcga_pub
67                         kirc_tcga
68                         kirp_tcga
69                      lihc_amc_prv
70                        lihc_riken
71                         lihc_tcga
72                     lgg_ucsf_2014
73                        luad_broad
74                   luad_mskcc_2015
75                     luad_tcga_pub
76                         luad_tcga
77                          luad_tsp
78                     lusc_tcga_pub
79                         lusc_tcga
80                         dlbc_tcga
81                       mpnst_mskcc
82                   plmeso_nyu_2015
83                  mcl_idibips_2013
84                    mbl_broad_2012
85                          mbl_icgc
86                          mbl_pcgp
87                skcm_broad_dfarber
88                   lgggbm_tcga_pub
89                         meso_tcga
90                    prad_su2c_2015
91                          mm_broad
92                    ccrcc_irc_2014
93                     brca_igr_2015
94                    mds_tokyo_2011
95                    cellline_nci60
96                   npc_nusingapore
97                      nbl_amc_2012
98                 nbl_ucologne_2015
99                     nepc_wcm_2016
100             hnsc_mdanderson_2013
101                      ov_tcga_pub
102                          ov_tcga
103            nsclc_tcga_broad_2016
104                        paad_icgc
105                paad_qcmg_uq_2016
106                        paad_tcga
107                   paad_utsw_2015
108                   panet_jhu_2011
109                    thca_tcga_pub
110            es_dfarber_broad_2014
111                        pcpg_tcga
112               thyroid_mskcc_2016
113                  pcnsl_mayo_2015
114                  prad_broad_2013
115                       prad_broad
116                       prad_fhcrc
117                       prad_mskcc
118                    prad_tcga_pub
119                        prad_tcga
120                  prad_mskcc_2014
121 prad_mskcc_cheny1_organoids_2014
122                        prad_mich
123                   hnc_mskcc_2016
124            nccrcc_genentech_2014
125                     rms_nih_2014
126                       sarc_mskcc
127                        sarc_tcga
128                       skcm_broad
129                        skcm_tcga
130                        skcm_yale
131                       scco_mskcc
132                       sclc_clcgp
133                         sclc_jhu
134               sclc_ucologne_2015
135            stad_pfizer_uhongkong
136                    stad_tcga_pub
137                        stad_tcga
138                      stad_utokyo
139                   stad_uhongkong
140                    stes_tcga_pub
141                        tgct_tcga
142                     tet_nci_2014
143                        thym_tcga
144                        thca_tcga
145                  urcc_mskcc_2016
146                     ucs_jhu_2014
147                         ucs_tcga
148                    ucec_tcga_pub
149                        ucec_tcga
150                         uvm_tcga
                                                                                    name
1                   Acinar Cell Carcinoma of the Pancreas (Johns Hopkins, J Pathol 2014)
2                                               Acute Myeloid Leukemia (TCGA, NEJM 2013)
3                                             Acute Myeloid Leukemia (TCGA, Provisional)
4                                  Adenoid Cystic Carcinoma (FMI, Am J Surg Pathl. 2014)
5                                   Adenoid Cystic Carcinoma (MDA, Clin Cancer Res 2015)
6                                       Adenoid Cystic Carcinoma (MSKCC, Nat Genet 2013)
7                                        Adenoid Cystic Carcinoma (Sanger/MDA, JCI 2013)
8                         Adenoid Cystic Carcinoma of the Breast (MSKCC, J Pathol. 2015)
9                                           Adrenocortical Carcinoma (TCGA, Provisional)
10                                                 Bladder Cancer (MSKCC, Eur Urol 2014)
11                                                      Bladder Cancer (MSKCC, JCO 2013)
12                          Bladder Cancer, Plasmacytoid Variant (MSKCC, Nat Genet 2016)
13                                    Bladder Urothelial Carcinoma (BGI, Nat Genet 2013)
14                Bladder Urothelial Carcinoma (Dana Farber & MSKCC, Cancer Discov 2014)
15                                      Bladder Urothelial Carcinoma (TCGA, Nature 2014)
16                                      Bladder Urothelial Carcinoma (TCGA, Provisional)
17                                          Brain Lower Grade Glioma (TCGA, Provisional)
18                               Breast Cancer (METABRIC, Nature 2012 & Nat Commun 2016)
19                             Breast Invasive Carcinoma (British Columbia, Nature 2012)
20                                        Breast Invasive Carcinoma (Broad, Nature 2012)
21                                       Breast Invasive Carcinoma (Sanger, Nature 2012)
22                                           Breast Invasive Carcinoma (TCGA, Cell 2015)
23                                         Breast Invasive Carcinoma (TCGA, Nature 2012)
24                                         Breast Invasive Carcinoma (TCGA, Provisional)
25                      Breast cancer patient xenografts (British Columbia, Nature 2014)
26                           Cancer Cell Line Encyclopedia (Novartis/Broad, Nature 2012)
27  Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (TCGA, Provisional)
28              Cholangiocarcinoma (National Cancer Centre of Singapore, Nat Genet 2013)
29                 Cholangiocarcinoma (National University of Singapore, Nat Genet 2012)
30                                                Cholangiocarcinoma (TCGA, Provisional)
31                                       Chronic Lymphocytic Leukemia (Broad, Cell 2013)
32                                     Chronic Lymphocytic Leukemia (IUOPA, Nature 2015)
33                             Clear Cell Renal Cell Carcinoma (U Tokyo, Nat Genet 2013)
34                                   Colorectal Adenocarcinoma (DFCI, Cell Reports 2016)
35                                    Colorectal Adenocarcinoma (Genentech, Nature 2012)
36                                         Colorectal Adenocarcinoma (TCGA, Nature 2012)
37                                         Colorectal Adenocarcinoma (TCGA, Provisional)
38                          Colorectal Adenocarcinoma Triplets (MSKCC, Genome Biol 2014)
39                                Cutaneous T Cell Lymphoma (Columbia U, Nat Genet 2015)
40                        Cutaneous squamous cell carcinoma (DFCI, Clin Cancer Res 2015)
41                               Desmoplastic Melanoma (Broad Institute, Nat Genet 2015)
42                                      Diffuse Large B-Cell Lymphoma (Broad, PNAS 2012)
43                                     Esophageal Adenocarcinoma (Broad, Nat Genet 2013)
44                                              Esophageal Carcinoma (TCGA, Provisional)
45                                Esophageal Squamous Cell Carcinoma (ICGC, Nature 2014)
46                             Esophageal Squamous Cell Carcinoma (UCLA, Nat Genet 2014)
47                                    Ewing Sarcoma (Institut Cuire, Cancer Discov 2014)
48                                      Gallbladder Carcinoma (Shanghai, Nat Genet 2014)
49                                            Gastric Adenocarcinoma (TMUCIH, PNAS 2015)
50                  Genomic Hallmarks of Prostate Adenocarcinoma (CPC-GENE, Nature 2017)
51                                                        Glioblastoma (TCGA, Cell 2013)
52                                                      Glioblastoma (TCGA, Nature 2008)
53                                           Glioblastoma Multiforme (TCGA, Provisional)
54                           Head and Neck Squamous Cell Carcinoma (Broad, Science 2011)
55                   Head and Neck Squamous Cell Carcinoma (Johns Hopkins, Science 2011)
56                             Head and Neck Squamous Cell Carcinoma (TCGA, Nature 2015)
57                             Head and Neck Squamous Cell Carcinoma (TCGA, Provisional)
58                                     Hepatocellular Adenoma (Inserm, Cancer Cell 2014)
59                         Hypodiploid Acute Lymphoid Leukemia (St Jude, Nat Genet 2013)
60          Infant MLL-Rearranged Acute Lymphoblastic Leukemia (St Jude, Nat Genet 2015)
61                                                Insulinoma (Shanghai, Nat Commun 2013)
62            Intrahepatic Cholangiocarcinoma (Johns Hopkins University, Nat Genet 2013)
63                                           Kidney Chromophobe (TCGA, Cancer Cell 2014)
64                                                Kidney Chromophobe (TCGA, Provisional)
65                               Kidney Renal Clear Cell Carcinoma (BGI, Nat Genet 2012)
66                                 Kidney Renal Clear Cell Carcinoma (TCGA, Nature 2013)
67                                 Kidney Renal Clear Cell Carcinoma (TCGA, Provisional)
68                             Kidney Renal Papillary Cell Carcinoma (TCGA, Provisional)
69                                 Liver Hepatocellular Carcinoma (AMC, Hepatology 2014)
70                                Liver Hepatocellular Carcinoma (RIKEN, Nat Genet 2012)
71                                    Liver Hepatocellular Carcinoma (TCGA, Provisional)
72                                                Low-Grade Gliomas (UCSF, Science 2014)
73                                                Lung Adenocarcinoma (Broad, Cell 2012)
74                                                      Lung Adenocarcinoma (MSKCC 2015)
75                                               Lung Adenocarcinoma (TCGA, Nature 2014)
76                                               Lung Adenocarcinoma (TCGA, Provisional)
77                                                Lung Adenocarcinoma (TSP, Nature 2008)
78                                      Lung Squamous Cell Carcinoma (TCGA, Nature 2012)
79                                      Lung Squamous Cell Carcinoma (TCGA, Provisional)
80                   Lymphoid Neoplasm Diffuse Large B-cell Lymphoma (TCGA, Provisional)
81                       Malignant Peripheral Nerve Sheath Tumor (MSKCC, Nat Genet 2014)
82                                 Malignant Pleural Mesothelioma (NYU, Cancer Res 2015)
83                                             Mantle Cell Lymphoma (IDIBIPS, PNAS 2013)
84                                                  Medulloblastoma (Broad, Nature 2012)
85                                                   Medulloblastoma (ICGC, Nature 2012)
86                                                   Medulloblastoma (PCGP, Nature 2012)
87                                             Melanoma (Broad/Dana Farber, Nature 2012)
88                                        Merged Cohort of LGG and GBM (TCGA, Cell 2016)
89                                                      Mesothelioma (TCGA, Provisional)
90          Metastatic Prostate Cancer, SU2C/PCF Dream Team (Robinson et al., Cell 2015)
91                                            Multiple Myeloma (Broad, Cancer Cell 2014)
92      Multiregion Sequencing of Clear Cell Renal Cell Carcinoma (IRC, Nat Genet 2014).
93                        Mutational profiles of metastatic breast cancer (France, 2016)
94                                                   Myelodysplasia (Tokyo, Nature 2011)
95                                             NCI-60 Cell Lines (NCI, Cancer Res. 2012)
96                                  Nasopharyngeal Carcinoma (Singapore, Nat Genet 2014)
97                                            Neuroblastoma (AMC Amsterdam, Nature 2012)
98                                                 Neuroblastoma (Broad, Nat Genet 2013)
99                            Neuroendocrine Prostate Cancer (Trento/Cornell/Broad 2016)
100                       Oral Squamous Cell Carcinoma (MD Anderson, Cancer Discov 2013)
101                                Ovarian Serous Cystadenocarcinoma (TCGA, Nature 2011)
102                                Ovarian Serous Cystadenocarcinoma (TCGA, Provisional)
103                                               Pan-Lung Cancer (TCGA, Nat Genet 2016)
104                                        Pancreatic Adenocarcinoma (ICGC, Nature 2012)
105                                        Pancreatic Adenocarcinoma (QCMG, Nature 2016)
106                                        Pancreatic Adenocarcinoma (TCGA, Provisional)
107                                            Pancreatic Cancer (UTSW, Nat Commun 2015)
108            Pancreatic Neuroendocrine Tumors (Johns Hopkins University, Science 2011)
109                                        Papillary Thyroid Carcinoma (TCGA, Cell 2014)
110                                   Pediatric Ewing Sarcoma (DFCI, Cancer Discov 2014)
111                               Pheochromocytoma and Paraganglioma (TCGA, Provisional)
112               Poorly-Differentiated and Anaplastic Thyroid Cancers (MSKCC, JCI 2016)
113          Primary Central Nervous System Lymphoma (Mayo Clinic, Clin Cancer Res 2015)
114                                   Prostate Adenocarcinoma (Broad/Cornell, Cell 2013)
115                              Prostate Adenocarcinoma (Broad/Cornell, Nat Genet 2012)
116                          Prostate Adenocarcinoma (Fred Hutchinson CRC, Nat Med 2016)
117                                    Prostate Adenocarcinoma (MSKCC, Cancer Cell 2010)
118                                            Prostate Adenocarcinoma (TCGA, Cell 2015)
119                                          Prostate Adenocarcinoma (TCGA, Provisional)
120                                 Prostate Adenocarcinoma CNA study (MSKCC, PNAS 2014)
121                                 Prostate Adenocarcinoma Organoids (MSKCC, Cell 2014)
122                          Prostate Adenocarcinoma, Metastatic (Michigan, Nature 2012)
123                    Recurrent and Metastatic Head & Neck Cancer (JAMA Oncology, 2016)
124                           Renal Non-Clear Cell Carcinoma (Genentech, Nat Genet 2014)
125                                           Rhabdomyosarcoma (NIH, Cancer Discov 2014)
126                                                Sarcoma (MSKCC/Broad, Nat Genet 2010)
127                                                          Sarcoma (TCGA, Provisional)
128                                           Skin Cutaneous Melanoma (Broad, Cell 2012)
129                                          Skin Cutaneous Melanoma (TCGA, Provisional)
130                                       Skin Cutaneous Melanoma (Yale, Nat Genet 2012)
131                            Small Cell Carcinoma of the Ovary (MSKCC, Nat Genet 2014)
132                                       Small Cell Lung Cancer (CLCGP, Nat Genet 2012)
133                               Small Cell Lung Cancer (Johns Hopkins, Nat Genet 2012)
134                                      Small Cell Lung Cancer (U Cologne, Nature 2015)
135                              Stomach Adenocarcinoma (Pfizer and UHK, Nat Genet 2014)
136                                           Stomach Adenocarcinoma (TCGA, Nature 2014)
137                                           Stomach Adenocarcinoma (TCGA, Provisional)
138                                     Stomach Adenocarcinoma (U Tokyo, Nat Genet 2014)
139                                         Stomach Adenocarcinoma (UHK, Nat Genet 2011)
140                          TCGA data for Esophagus-Stomach Cancers (TCGA, Nature 2017)
141                                      Testicular Germ Cell Cancer (TCGA, Provisional)
142                                       Thymic Epithelial Tumors (NCI, Nat Genet 2014)
143                                                          Thymoma (TCGA, Provisional)
144                                                Thyroid Carcinoma (TCGA, Provisional)
145                                       Unclassified Renal Cell Carcinoma (MSKCC 2016)
146                   Uterine Carcinosarcoma (Johns Hopkins University, Nat Commun 2014)
147                                           Uterine Carcinosarcoma (TCGA, Provisional)
148                             Uterine Corpus Endometrial Carcinoma (TCGA, Nature 2013)
149                             Uterine Corpus Endometrial Carcinoma (TCGA, Provisional)
150                                                   Uveal Melanoma (TCGA, Provisional)
                                                                                                                                                                                                                                                                                                                                    description
1                                                                                                                                                                                                                        Mutation data from whole exome sequencing of 23 surgically resected pancreatic carcinomas with acinar differentiation.
2                                                                                                                                 TCGA Acute Myeloid Leukemia, analysis of 200 adult cases; raw data at the <A HREF="https://tcga-data.nci.nih.gov/tcga/tcgaCancerDetails.jsp?diseaseType=LAML&diseaseName=Acute%20Myeloid%20Leukemia">NCI</A>.
3                                                                                                                                                                                                                                                TCGA Acute Myeloid Leukemia; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
4                                                                                                                                                                                                                                                                                        Comprehensive genomic profiling of 28 metastatic ACCs.
5                                                                                                                                                                                                                                                    WGS of 21 salivary ACCs and targeted molecular analyses of a validation set (81 patients).
6                                                                                                                                                                                                                                                                                        Exome profiling of 60 adenoid cystic carcinoma samples
7                                                                                                                                                                                                                                                                                                            Whole exome sequencing of 24 ACCs.
8                                                                                                                                                                                                                                                                                                    Whole exome sequencing of 12 breast AdCCs.
9                                                                                                                                                                                                                                              TCGA Adrenocortical Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
10                                                                                                                                                                     Genomic Predictors of Survival in Patients with High-grade Urothelial Carcinoma of the Bladder. Targeted sequencing of 109 tumor samples (MSKCC, European Urology 2014).
11                                                                                                                                                                                                           Comprehensive profiling of 97 bladder cancer samples, including targeted sequencing of 15 cancer genes. Iyer et al., JCO in press.
12                                                                                                                                                                                                                                            Genomic profiling of plasmacytoid-variant (signet ring cell) tumors of the bladder, published set
13                                                                                                                                                                                                                                                            Exome and whole-genome sequencing of 99 bladder cancer samples. Generated by BGI.
14                                                                                                                                                                                                                                                              Whole exome sequencing of 50 patients with muscle invasive urothelial carcinoma
15                                                                                                                                                                                                                                                                            TCGA Bladder Cancer, containing 131 samples; raw data at the NCI.
16                                                                                                                                                                                                                                         TCGA Bladder Urothelial Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
17                                                                                                                                                                                                                                             TCGA Brain Lower Grade Glioma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
18                                                                                                                                                                                                         The genomic profiles (somatic mutations [targeted sequencing], copy number alterations, and gene expression) of 2509 breast cancers.
19                                                                                                                                                                                                                               Comprehensive profiling of 65 breast cancer samples. Generated by the British Columbia Cancer Research Centre.
20                                                                                                                                                                                                                                                      Comprehensive profiling of 103 breast cancer samples. Generated by the Broad Institute.
21                                                                                                                                                                                                                                                     Comprehensive profiling of 100 breast cancer samples. Generated by the Sanger Institute.
22                                                                                                                                                                                                     <a href="http://cancergenome.nih.gov/">The Cancer Genome Atlas (TCGA)</a> Breast Invasive Carcinoma project. 817 cases (TCGA Cell 2015).
23                                                                                   <a href="http://cancergenome.nih.gov/">The Cancer Genome Atlas (TCGA)</a> Breast Invasive Carcinoma project. 825 cases.<br><i>Nature 2012.</i> <a href="https://tcga-data.nci.nih.gov/docs/publications/brca_2012/">Raw data via the TCGA Data Portal</a>.
24                                                                                                                                                                                                                                            TCGA Breast Invasive Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
25                                                                                                                                                                                                                                                                              Dynamics of genomic clones in breast cancer patient xenografts.
26                                                                                                                            Cancer Cell Line Encyclopedia from the Broad Institute and Novartis, containing 883 samples; raw data at the <A HREF="http://www.broadinstitute.org/ccle/data/browseData?conversationPropagation=begin">CCLE</A>.
27                                                                                                                                                                                                     TCGA Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
28                                                                                                                                                                                                                 Exome sequencing of 15 cholangiocarcinoma cases from the National Cancer Centre of Singapore to study the somatic mutations.
29                                                                                                                                                                                                            Exome Sequencing for Opisthorchis viverrini-related cholangiocarcinoma in 8 O.viverrini-related tumors and matched normal tissue.
30                                                                                                                                                                                                                                                   TCGA Cholangiocarcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
31                                                                                                                                                                                                                                                                       Exome sequencing of 160 CLL samples. Generated by the Broad Institute.
32                                                                                                                                                                                                                                  Mutation data from whole-genome or whole-exome sequencing (WGS/WXS) of 428 CLL, 54 MBL, and 24 SLL samples.
33                                                                                                                                                                                                                                Mutation data from whole genome and/or whole exome sequencing of 106 clear-cell renal cell carcinoma samples.
34                                                                                                                                                                                                                                                         Whole-exome sequencing of 619 colorectal cancers with clinicopathologic annotations.
35                                                                                                                                                                                                                                                                  Comprehensive profiling of 72 colon cancer samples. Generated by Genentech.
36                                                                                                 <a href="http://cancergenome.nih.gov/">The Cancer Genome Atlas (TCGA)</a> Colorectal Cancer project. <br><i>Nature 2012.</i> <a href="https://tcga-data.nci.nih.gov/docs/publications/coadread_2012/">Raw data via the TCGA Data Portal</a>.
37                                                                                                                                                                                                                                            TCGA Colorectal Adenocarcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
38                                                                                                                                                                                             Colon Trios data from 69 Patients each with a  primary and metastatic tumor. (Primary / Met) (David Solit / Evi Vakiani / Michael Berger, MSKCC)
39                                                                                                                                                                                Whole-Exome Sequencing (WXS) of tumor-normal sample pairs from 25 patients with Sezary Syndrome and 17 patients with other Cutaneous T Cell Lymphoma (CTCLs).
40                                                                                                                                                                                                                                           Targeted sequencing of 504 cancer-associated genes in 29 cutaneous squamous cell carcinoma samples
41                                                                                                                                                                                                                                                          Mutation data from Exome/Whole Genome sequencing of 20 desmoplastic melanoma cases.
42                                                                                                                                                                                                                                                                                                  Whole exome sequencing of 58 DLBCL samples.
43                                                                                                                                                                                                                                                   Comprehensive profiling of 149 esophageal adenocarcinoma samples from the Broad Institute.
44                                                                                                                                                                                                                                                TCGA Esophageal Carcinoma ; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
45                                                                                                                                                                                                                                                             WGS and WES of 88 esophageal squamous cell carcinoma samples. Generated by ICGC.
46                                                                                                                                                                                                                    Whole exome sequencing (WXS) or targeted deep sequencing (TDS) of 139 paired esophageal squamous cell carcinoma patients.
47                                                                                                                                                            Mutation data from whole-genome sequencing of 112 Ewing sarcoma samples and matched germ line DNA. <a href="http://cancerdiscovery.aacrjournals.org/content/4/11/1342/suppl/DC1">
48                                                                                                                                                                                                                                             Mutation data from whole exome sequencing of 32 gallbladder carcinoma tumors with paired normals
49                                                                                                                                                                                                                                          Whole-exome sequencing on 78 Gastric Adenocarcinoma of differing histologies and anatomic locations
50                                                                                                                                                                                                              Comprehensive genomic profiling of 477 Prostate Adenocarcinoma samples from CPC-GENE and public data sets, including TCGA-PRAD.
51                                                                                                                                                      <a href="http://cancergenome.nih.gov/">The Cancer Genome Atlas (TCGA)</a> Glioblastoma project.<br> <a href="http://tcga-data.nci.nih.gov/tcga/">Raw data via the TCGA Data Portal</a>.
52                                                                                             <a href="http://cancergenome.nih.gov/">The Cancer Genome Atlas (TCGA)</a> Glioblastoma project. 206 primary glioblastoma samples.<br> <a href="https://tcga-data.nci.nih.gov/docs/publications/gbm_2008/">Raw data via the TCGA Data Portal</a>.
53                                                                                                                                                                                                                                              TCGA Glioblastoma Multiforme; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
54                                                                                                                                                                                                                                        Comprehensive profiling of 74 head and neck squamous cell carcinoma samples from the Broad Institute.
55                                                                                                                                                                                                                                              Comprehensive profiling of 32 head and neck squamous cell carcinoma samples from Johns Hopkins.
56                                                                                                           TCGA Head and Neck Squamous Cell Carcinoma, containing 279 samples; raw data at the <A HREF="https://tcga-data.nci.nih.gov/tcga/tcgaCancerDetails.jsp?diseaseType=HNSC&diseaseName=Head and Neck Squamous Cell Carcinoma">NCI</A>.
57                                                                                                                                                                                                                                TCGA Head and Neck Squamous Cell Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
58                                                                                                                                                                                                                                            Mutation data from whole-exome sequencing (WXS) of 46 liver tumor and corresponding nontumor DNA.
59                                                                                                                                                                                                                                                                                                          Exome sequencing of 44 ALL samples.
60                                                                                                                                                                                                                                     Whole genome sequencing (WGS) of 22 infant MLL-rearranged acute lymphoblastic leukemia (MLL-R ALL) cases
61                                                                                                                                                                                               Whole exome sequencing of 10 benign insulinoma tumors. <A HREF="http://www.nature.com/ncomms/2013/131210/ncomms3810/extref/ncomms3810-s1.pdf">
62                                                                                                                                                                                                                                             Exome Sequencing of 32 intrahepatic cholangiocarcinoma cases and 8 gall bladder carcinoma cases.
63                                                                                                                                                                         TCGA Kidney Chromophobe; raw data at the <A HREF="https://tcga-data.nci.nih.gov/tcga/tcgaCancerDetails.jsp?diseaseType=KICH&diseaseName=Kidney Chromophobe">NCI</A>.
64                                                                                                                                                                                                                                                   TCGA Kidney Chromophobe; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
65                                                                                                                                                                                                                                                  Comprehensive sequencing of 98 clear cell kidney cancer samples. Generated by BGI-Shenzhen.
66                                                                                                                   TCGA Kidney Renal Clear Cell Carcinoma, containing 499 samples; raw data at the <A HREF="https://tcga-data.nci.nih.gov/tcga/tcgaCancerDetails.jsp?diseaseType=KIRC&diseaseName=Kidney Renal Clear Cell Carcinoma">NCI</A>.
67                                                                                                                                                                                                                                    TCGA Kidney Renal Clear Cell Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
68                                                                                                                                                                                                                                TCGA Kidney Renal Papillary Cell Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
69                                                                                                                                                                                                                                                      Liver Hepatocellular Carcinoma from Asan Medical Center, Korea, containing 231 samples.
70                                                                                                                                                                                                                                                                   Whole-genome sequencing of 27 hepatocellular carcinoma samples from RIKEN.
71                                                                                                                                                                                                                                       TCGA Liver Hepatocellular Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
72                                                                                                                                                                                                                                                                    Mutation data from whole exome sequencing of 23 grade II glioma patients.
73                                                                                                                                                                                                                                                Comprehensive profiling of 183 lung adenocarcinoma samples. Generated by the Broad Institute.
74                                                                                                                                                                                                                                                             Whole-exome sequencing of non small cell lung cancers treated with pembrolizumab
75                                                                                                                                                TCGA Lung Adenocarcinoma, containing 230 samples; raw data at the <A HREF="https://tcga-data.nci.nih.gov/tcga/tcgaCancerDetails.jsp?diseaseType=LUAD&diseaseName=Lung Adenoarcinoma">NCI</A>.
76                                                                                                                                                                                                                                                  TCGA Lung Adenocarcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
77                                                                                                                                                                                                                                                            Targeted sequencing of 163 lung adenocarcinoma samples. Generated by WashU/Broad.
78                                                                                <a href="http://cancergenome.nih.gov/">The Cancer Genome Atlas (TCGA)</a> Lung Squamous Cell Carcinoma project. 178 cases.<br><i>Nature 2012.</i> <a href="https://tcga-data.nci.nih.gov/docs/publications/lusc_2012/">Raw data via the TCGA Data Portal</a>.
79                                                                                                                                                                                                                                         TCGA Lung Squamous Cell Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
80                                                                                                                                                                                                                      TCGA Lymphoid Neoplasm Diffuse Large B-cell Lymphoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
81                                                                                                                                                                                                                                                                              Exome profiling of 17 malignant peripheral nerve sheath tumors.
82                                                                                                                                                                                                                          Mutation data from whole-exome sequencing of 22 malignant pleural mesotheliomas (PLMESO) and matched blood samples.
83                                                                                                                                                                                                                                                                                  Whole exome sequencing of 29 primary mantle cell lymphomas.
84                                                                                                                                                                                                                                                              Comprehensive profiling of 92 medulloblastoma samples from the Broad Institute.
85                                                                                                                                                                                                                                                                                              125 Medulloblastoma tumor / normal pairs. ICGC.
86                                                                                                                                                   Whole genome sequencing of 37 medulloblastoma samples from the Pediatric Cancer Genome Project (PCGP), a joint project by St. Jude Children's Research Hospital and Washington University.
87                                                                                                                                                                                                                                                             Somatic Mutation data from 25 Whole Genome Sequenced metastatic melanoma samples
88                                                                                                                                                                                                                                                                                           Whole-exome sequencing from TCGA LGG and GBM cases
89                                                                                                                                                                                                                                                         TCGA Mesothelioma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
90                                                                                                                                                                                                                                                  Comprehensive analysis of 150 metastatic prostate cancer samples by the SU2C/PCF Dream Team
91                                                                                                                                                                                                                                                                                            Exome sequencing of 205 multiple myeloma samples.
92                                                                                                                                                                                                                                             Mutation data from multi region exome sequencing of 10 clear cell renal cell carcinomas (ccRCCs)
93                                                       Whole-exome sequencing was performed on 216 tumor-normal (blood) pairs from metastatic breast cancer patients who underwent a biopsy in the context of the SAFIR01/SAFIR02 (Unicancer, France), SHIVA (Institut Curie, France) or MOSCATO (Gustave Roussy, France) prospective trials.
94                                                                                                                                                                                                                                                            Whole exome sequencing of 29 myelodysplasia samples from the University of Tokyo.
95                                                                                                                                                                                                                         NCI-60 cell line project; raw data at <A HREF="http://discover.nci.nih.gov/cellminer/loadDownload.do">CellMiner</A>.
96                                                                                                                                                                                            Whole genome sequencing of 56 NPC tumor / normal pairs. Generated by the Cancer Science Institute of Singapore, National University of Singapore.
97                                                                                                                                                                                                                                             Whole genome sequencing of 87 neuroblastoma samples from the Academic Medical Center, Amsterdam.
98                                                                                                                                                                                                                                                                       Mutation data from whole-genome sequencing of 56 neuroblastoma samples
99                                                                                                                                                                  Whole exome and RNA Seq data of castration resistant adenocarcinoma and castration resistant neuroendocrine prostate cancer (somatic mutations and copy number aberrations)
100                                                                                                                                                                                                                                                        Comprehensive profiling of 40 oral squamous cell carcinoma samples from MD Anderson.
101                                                                                                           <a href="http://cancergenome.nih.gov/">The Cancer Genome Atlas (TCGA)</a> Serous Ovarian Cancer project. 489 cases.<br> <a href="https://tcga-data.nci.nih.gov/docs/publications/ov_2011/">Raw data via the TCGA Data Portal</a>.
102                                                                                                                                                                                                                                   TCGA Ovarian Serous Cystadenocarcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
103                                                                                                                                                                                                                                                            Somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas.
104                                                                                                                                                                                                                                                                 Comprehensive profiling of 99 pancreatic cancer samples. Generated by ICGC.
105                                                                                                                          342 primary tumours and 41 patient-derived cell lines underwent whole genome sequencing (WGS) when tumour cellularity was >40% (n=179), or deep-exome sequencing (n=204) for samples with a cellularity of 12-40%.
106                                                                                                                                                                                                                                           TCGA Pancreatic Adenocarcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
107                                                                                                                                                                                                                                            Whole exome sequencing of 109 micro-dissected pancreatic cancer cases and normal control tissue.
108                                                                                                                                                                                                Whole exome sequencing of 10 pancreatic neuroendocrine tumor patients. <A HREF="https://www.sciencemag.org/content/331/6021/1199/suppl/DC1">
109                                                                                                                                      TCGA Papillary Thyroid Carcinoma, containing 230 samples; raw data at the <A HREF="https://tcga-data.nci.nih.gov/tcga/tcgaCancerDetails.jsp?diseaseType=THCA&diseaseName=Thyroid%20carcinoma">NCI</A>.
110                                                                                                                                                                                                                                                              Whole exome sequencing of 96 pediatric Ewing Sarcoma tumors and 11 cell lines.
111                                                                                                                                                                                                                                  TCGA Pheochromocytoma and Paraganglioma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
112                                                                                                                                                                                                                          Next generation sequencing (MSK-IMPACT) of 84 poorly-differentiated (PDTC) and 33 anaplastic thyroid cancers (ATC)
113                                                                                                                                                                                                              Mutation data from whole exome sequencing (WXS) of 10 immunocompetent primary central nervous system lymphoma (PCNSL) samples.
114                                                                                                                                                                                             Comprehensive profiling of 57 prostate cancer samples. Generated by Levi Garraway's lab at the Broad Institute and Mark Rubin's lab at Cornell.
115                                                                                                                                                                                            Comprehensive profiling of 112 prostate cancer samples. Generated by Levi Garraway's lab at the Broad Institute and Mark Rubin's lab at Cornell.
116                                                                                                                                                                                                          Comprehensive profiling of prostate cancer samples. Generated by Peter Nelson's lab at the Fred Hutchinson Cancer Research Center.
117 MSKCC Prostate Oncogenome Project. 181 primary, 37 metastatic prostate cancer samples, 12 prostate cancer cell lines and xenografts.<br><a href="http://cbio.mskcc.org/cancergenomics/prostate/data/">Normalized flat data files</a>. <a href="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21032">Raw data via GEO (GSE21032)</a>.
118                                                                                                                                                                          Integrated profiling of 333 primary prostate adenocarcinoma samples; raw data at the <A HREF="https://tcga-data.nci.nih.gov/docs/publications/prad_2015/">NCI</A>.
119                                                                                                                                                                                                                                             TCGA Prostate Adenocarcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
120                                                                                                                                                              Copy-number profiling of 103 primary prostate cancer samples from MSKCC. <a href="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE54691">Raw data via GEO (GSE54691)</a>.
121                                                                                                                                                                                                                                                                           Exome profiling of prostate cancer samples and matched organoids.
122                                                                                                                    Comprehensive profiling of 61 prostate cancer samples, including 50 metastatic CRPCs and 11 high-grade localized prostate cancers. Generated by Arul Chinnaiyan's and Scott Tomlins' labs at the University of Michigan.
123                                                                                                                                                                                                                                                 Targeted sequencing of 151 patients with advanced, treatment resistant head and neck tumors
124                                                                                                                                                                                                                                                                    Exome sequencing of 139 Renal Non-Clear Cell Carcinoma (NCCRCC) samples.
125                                                                                                                                                                                                                                                                           Mutation data from WGS and/or WXS of 43 rhabdomyosarcoma samples.
126           The Sarcoma Genome Project, <a href="http://www.mskcc.org/">MSKCC</a> and <a href="http://www.broadinstitute.org/">The Broad Institute</a>. 207 high-grade adult soft tissue sarcomas across seven subtypes of disease.<br> <a href="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21124">Raw data via GEO (GSE21124)</a>.
127                                                                                                                                                                                                                                                             TCGA Sarcoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
128                                                                                                                                                                                                                                                          Comprehensive profiling of 121 melanoma samples. Generated by the Broad Institute.
129                                                                                                                                                                                                                                             TCGA Skin Cutaneous Melanoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
130                                                                                                                                                                                                                                                                                 Exome sequencing of 91 melanoma samples. Generated by Yale.
131                                                                                                                                                                                                                                                                                                     Targeted sequencing of 12 SCCO samples.
132                                                                                                                                                                                                                         Comprehensive profiling of 29 small cell lung cancer samples. Generated by the Clinical Lung Cancer Genome Project.
133                                                                                                                                                                                                      Comprehensive profiling of 36 primary human SCLC tumors and 17 matched SCLC and lymphoblastoid cell lines. Generated by Johns Hopkins.
134                                                                                                                                                                                                                                                                                    Comprehensive WGS profiling of 110 human SCLC specimens.
135                                                                                                                                                                                                                                              Whole genome sequencing of 100 tumor-normal pairs from the University of Hong Kong and Pfizer.
136                                                                                                                                                                                          TCGA Stomach Adenocarcinoma, containing 295 samples; raw data at the <A HREF="https://tcga-data.nci.nih.gov/docs/publications/stad_2014/">NCI</A>.
137                                                                                                                                                                                                                                              TCGA Stomach Adenocarcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
138                                                                                                                                                                                                                                      Whole exome sequencing of 30 diffuse-type gastric adenocarcinoma samples from the University of Tokyo.
139                                                                                                                                                                                                                                                                                              Exome sequencing of 22 gastric cancer samples.
140                                                                                                                                                                                                                                                                                                    TCGA data for Esophagus-Stomach Cancers.
141                                                                                                                                                                                                                                         TCGA Testicular Germ Cell Cancer; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
142                                                                                                                                                                                                                                                                                      Whole exome sequencing of 28 thymic epithelial tumors.
143                                                                                                                                                                                                                                                             TCGA Thymoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
144                                                                                                                                                                                                                                                   TCGA Thyroid Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
145                                                                                                                                                                                                                                                                                     Molecular Analysis of Unclassified Renal Cell Carcinoma
146                                                                                                                                           Whole exome sequencing (WXS) of 22 uterine carcinosarcoma/uterine malignant mixed Mullerian (UCS) tumors. <A HREF="http://www.nature.com/ncomms/2014/140919/ncomms6006/extref/ncomms6006-s1.pdf">
147                                                                                                                                                                                                                                              TCGA Uterine Carcinosarcoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
148                                                                                                                                                                            TCGA Uterine Corpus Endometrial Carcinoma, containing 373 samples; raw data at the <A HREF="https://tcga-data.nci.nih.gov/docs/publications/ucec_2013/">NCI</A>.
149                                                                                                                                                                                                                                TCGA Uterine Corpus Endometrial Carcinoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
150                                                                                                                                                                                                                                                      TCGA Uveal Melanoma; raw data at the <A HREF="https://tcga-data.nci.nih.gov/">NCI</A>.
> 
> # Set custom error plot message
> setPlotErrorMsg(mycgds, 'My message ...')
[1] "My message ..."
> 
> getCancerStudies(mycgds)
Warning in file(file, "rt") :
  InternetOpenUrl failed: 'Das Zeitlimit für den Vorgang wurde erreicht.'
Error in file(file, "rt") : cannot open the connection
Calls: getCancerStudies ... processURL -> processURL.CGDS -> read.table -> file
Execution halted