Nothing
gkmsvm_delta<- function( seqfile_allele1,
seqfile_allele2,
svmfnprfx,
outfile,
L=10,
K=6,
maxnmm=3,
maxseqlen=10000,
maxnumseq=1000000,
useTgkm=1,
alg=2,
addRC=TRUE,
usePseudocnt=FALSE,
batchSize=100000,
wildcardLambda=1.0,
wildcardMismatchM=2,
alphabetFN="NULL",
svseqfile=NA,
alphafile=NA,
outfile_allele1 = NA,
outfile_allele2 = NA
){
if(is.na(outfile_allele1)){
outfile_allele1 = tempfile()
}
if(is.na(outfile_allele2)){
outfile_allele2 = tempfile()
}
gkmsvm_classify(seqfile = seqfile_allele1, svmfnprfx = svmfnprfx, outfile = outfile_allele1,
L=L ,K=K, maxnmm=maxnmm,maxseqlen=maxseqlen,maxnumseq=maxnumseq,useTgkm=useTgkm,alg=alg,addRC=addRC,
usePseudocnt=usePseudocnt,batchSize=batchSize,wildcardLambda=wildcardLambda,wildcardMismatchM=wildcardMismatchM,
alphabetFN=alphabetFN,svseqfile=svseqfile,alphafile=alphafile)
gkmsvm_classify(seqfile = seqfile_allele2, svmfnprfx = svmfnprfx, outfile = outfile_allele2,
L=L ,K=K, maxnmm=maxnmm,maxseqlen=maxseqlen,maxnumseq=maxnumseq,useTgkm=useTgkm,alg=alg,addRC=addRC,
usePseudocnt=usePseudocnt,batchSize=batchSize,wildcardLambda=wildcardLambda,wildcardMismatchM=wildcardMismatchM,
alphabetFN=alphabetFN,svseqfile=svseqfile,alphafile=alphafile)
s1 = utils::read.delim(outfile_allele1, header=FALSE)
s2 = utils::read.delim(outfile_allele2, header=FALSE)
res = as.numeric(s2[,2])-as.numeric(s1[,2]); names(res)=as.character(s1[,1]);
utils::write.table(cbind(as.character(s1[,1]), res), file = outfile, quote = FALSE, row.names=FALSE, col.names = FALSE)
res=res;
}
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