Running examples in ‘fat2Lpoly-Ex.R’ failed
The error most likely occurred in:

> ### Name: fat2Lpoly
> ### Title: Two-locus Family-based Association Test with Polytomous Outcome
> ### Aliases: fat2Lpoly
> 
> ### ** Examples
> 
> path.data=paste(.libPaths()[which(unlist(lapply(.libPaths(),
+ function(x) length(grep("fat2Lpoly",dir(x)))))>0)],"/fat2Lpoly/extdata/",sep="")
> if(length(path.data)>1) path.data=path.data[length(path.data)]
> 
> snps.anal=c("snp3.loc2","snp4.loc2")
> microsat.names.loc2=c("2_3_mrk:","2_4_mrk:")
> 
> ############ design.endo2disease with conditioning on locus 1 ################
> ## Not run: 
> ##D joint.tests=list(c(2,5))
> ##D snp.names.mat=cbind(rep("snp4.loc1",length(snps.anal)),snps.anal)
> ##D microsat.names.mat=cbind(rep("1_4_mrk:",length(snps.anal)),microsat.names.loc2)
> ##D test=fat2Lpoly(pedfilenames=paste(path.data,c("loc1.ped","loc2.ped"),sep=""),
> ##D                datfilenames=paste(path.data,c("loc1.dat","loc2.dat"),sep=""),
> ##D 			   freq.data=paste(path.data,c("loc1.freq","loc2.freq"),sep=""),
> ##D                ibdfilenames=paste(path.data,c("loc1.ibd","loc2.ibd"),sep=""),
> ##D 		       snp.names.mat=snp.names.mat,ibd.loci=microsat.names.mat,
> ##D 		       joint.tests=joint.tests,contingency.file=TRUE,
> ##D 		       design.constraint=design.endo2disease,lc=1)
> ##D 
> ##D test$p.values.scores
> ## End(Not run)		   
> ###############################################################################
> 
> ################### design.endo2disease without conditioning ##################
> joint.tests=list(c(2,5))
> snp.names.mat=cbind(rep("snp4.loc1",length(snps.anal)),snps.anal)
> microsat.names.mat=cbind(rep("1_4_mrk:",length(snps.anal)),microsat.names.loc2)
> test=fat2Lpoly(pedfilenames=paste(path.data,c("loc1.ped","loc2.ped"),sep=""),
+                datfilenames=paste(path.data,c("loc1.dat","loc2.dat"),sep=""),
+ 			   freq.data=paste(path.data,c("loc1.freq","loc2.freq"),sep=""),
+                ibdfilenames=paste(path.data,c("loc1.ibd","loc2.ibd"),sep=""),
+ 		       snp.names.mat=snp.names.mat,ibd.loci=microsat.names.mat,
+ 		       joint.tests=joint.tests,contingency.file=FALSE,
+ 		       design.constraint=design.endo2disease)

Y1 data extracted from input files:    endo 
Y2 data extracted from input files:    pheno 

Warning in FUN(X[[i]], ...) : NAs introduced by coercion
Warning in FUN(X[[i]], ...) : NAs introduced by coercion
Warning in FUN(X[[i]], ...) : NAs introduced by coercion
Error in read.merlin.files(pedfilenames, datfilenames, freq.data, ibdfilenames) : 
  'list' object cannot be coerced to type 'double'
Calls: fat2Lpoly -> read.merlin.files
Execution halted