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--- re-building ‘localScorePackageDocumentation.Rmd’ using rmarkdown
localScore-package         package:localScore          R Documentation

_P_a_c_k_a_g_e _f_o_r _s_e_q_u_e_n_c_e _a_n_a_l_y_s_i_s _b_y _l_o_c_a_l _s_c_o_r_e

_D_e_s_c_r_i_p_t_i_o_n:

     Provides functionalities for:

        • calculating the local score

        • calculating statistical relevance (p-value) to find a local
          Score in a sequence of given distribution.

_D_e_t_a_i_l_s:

     Please refer to the vignette of this package or the manual for
     details on how to use this package.

_A_u_t_h_o_r(_s):

     Sebastian Simon, Sabine Mercier, David Robelin, Anne-Benedicte
     Urbano

     Maintainer: David Robelin david.robelin@inra.fr

_R_e_f_e_r_e_n_c_e_s:

     p-value:

        • An Improved Approximation For Assessing The Statistical
          Significance of molecular Sequence Features, Mercier and al
          2003

        • Exact distribution for the local score of one i.i.d. random
          sequence, Sabine Mercier and JJ Daudin, 2001

        • Limit Distributions of Maximal Segmental Score among
          Markov-Dependent Partial Sums, Karlin and Dembo 1992

        • Methods for assessing the statistical significance of
          molecular sequence features by using general scoring schemes,
          Karlin and al 1990

     local Score:

        • Detection de courts segments inverses dans les genomes:
          methodes et applications, David Robelin 2005

        • A Linear Time Algorithm for Finding All Maximal Scoring
          Subsequences, Constable and Bates 1985


dico                package:localScore                 R Documentation

_D_i_c_t_i_o_n_n_a_i_r_e

_D_e_s_c_r_i_p_t_i_o_n:

     Provides the score related to each base of the sequences.

_U_s_a_g_e:

     dico
     
_F_o_r_m_a_t:

     A score function for the 20 amino acid

_S_o_u_r_c_e:

     Kyte & Doolittle (1982) J. Mol. Biol. 157, 105-132

_E_x_a_m_p_l_e_s:

     data(dico)
     dico
     data(MidSeq)
     MidSeq
     MidSeqScore=CharSequence2ScoreSequence(MidSeq,dico)
     MidSeqScore[1:30]
     localScoreC(MidSeqScore)$localScore
     

Warning in localScoreC_double(seq.essai) :
  The mean of this sequence is greater than 0. The sequence may be trivial
Warning in localScoreC(C * seq.essai) :
  The mean of this sequence is greater than 0. The sequence may be trivial
Warning in localScoreC(C * seq.essai) :
  The mean of this sequence is greater than 0. The sequence may be trivial
Warning in localScoreC_double(seq.essai) :
  The mean of this sequence is greater than 0. The sequence may be trivial
Warning in automatic_analysis(sequences = list(x1 = seq.essai), distribution = proba_score,  :
  [Ignoring Sequence] sequence mean >= 0 and sequence length = 5000
Warning in localScoreC(SeqScore.S) :
  The mean of this sequence is greater than 0. The sequence may be trivial
! You can't use `macro parameter character #' in math mode.
l.411 \(ProbExtendedIntegerScore #
                                  > -10 -9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4...

Error: processing vignette ‘localScorePackageDocumentation.Rmd’ failed with diagnostics:
LaTeX failed to compile /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/localScore.Rcheck/vign_test/localScore/vignettes/localScorePackageDocumentation.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See localScorePackageDocumentation.log for more info.
--- failed re-building ‘localScorePackageDocumentation.Rmd’

SUMMARY: processing the following file failed:
  ‘localScorePackageDocumentation.Rmd’

Error: Vignette re-building failed.
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