setAnnotation: Fills in annotations of tagSNVs of a list of IBD segments

In hapFabia: hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data

Description

setAnnotation: R implementation of setAnnotation.

Fills in the tagSNV annotation of IBD segments given in an object of the class IBDsegmentList. The annotation must be given in a file where the first column contains the position of the SNV and the second the chromosome. The other columns give the annotation like "stop gain", "stop loss", "synonymous", "non-synonymous", "exonic", "intronic", "intergenic", "promotor", etc. However other annotations like whether the minor allele is identical to the Denisova or Neandertal base can be included.

Usage

## S4 method for signature 'IBDsegmentList,character'
setAnnotation(IBDsegmentList,filename)

Arguments

IBDsegmentList	object of class IBDsegmentList.
filename	File containing the SNV annotations, where the first column contains the SNV position and the second the chromosome.

Details

Implementation in R.

Value

object of class IBDsegmentList in which the annotation for the tagSNVs is set.

Author(s)

Sepp Hochreiter

References

S. Hochreiter et al., ‘FABIA: Factor Analysis for Bicluster Acquisition’, Bioinformatics 26(12):1520-1527, 2010.

See Also

IBDsegment-class, IBDsegmentList-class, analyzeIBDsegments, compareIBDsegmentLists, extractIBDsegments, findDenseRegions, hapFabia, hapFabiaVersion, hapRes, chr1ASW1000G, IBDsegmentList2excel, identifyDuplicates, iterateIntervals, makePipelineFile, matrixPlot, mergeIBDsegmentLists, mergedIBDsegmentList, plotIBDsegment, res, setAnnotation, setStatistics, sim, simu, simulateIBDsegmentsFabia, simulateIBDsegments, split_sparse_matrix, toolsFactorizationClass, vcftoFABIA

Examples

old_dir <- getwd()
setwd(tempdir())

data(hapRes)

res <- hapRes$res
sPF <- hapRes$sPF
annot <- hapRes$annot
nnL <- length(Z(res)[1,])
labelsA <- cbind(as.character(1:nnL),
   as.character(1:nnL),as.character(1:nnL),
   as.character(1:nnL))
resIBDsegmentList <-
  extractIBDsegments(res=res,sPF=sPF,
  annot=annot,chrom="1",labelsA=labelsA,
  ps=0.9,psZ=0.8,inteA=50,thresA=6,mintagSNVs=6,
  off=0,procMinIndivids=0.1,thresPrune=1e-3)


tagSNVPositions <-
   tagSNVPositions(resIBDsegmentList[[1]])
snvR <- sample(min(tagSNVPositions):max(tagSNVPositions),
   length(tagSNVPositions))
snvA <- sort(unique(c(tagSNVPositions,snvR)))

func = c("stopGain","stopLoss","synonymous",
   "non-synonymous","-","-","-","-","-","-")
for (i in 1:length(snvA)) {

if (i>1) {
write(paste(snvA[i],"1",sample(func,1),sep=" "),
   file="snvAnnotation.txt",ncolumns=100,append=TRUE)
} else {

write(paste(snvA[i],"1",sample(func,1),sep=" "),
   file="snvAnnotation.txt",ncolumns=100,append=FALSE)
}


}

tagSNVAnno(resIBDsegmentList[[1]])

resIBDsegmentList <- setAnnotation(resIBDsegmentList,
   filename="snvAnnotation.txt")

tagSNVAnno(resIBDsegmentList[[1]])

setwd(old_dir)

hapFabia documentation built on Nov. 8, 2020, 5:17 p.m.