setAnnotation {hapFabia} | R Documentation |
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.
## S4 method for signature 'IBDsegmentList,character' setAnnotation(IBDsegmentList,filename)
IBDsegmentList |
object of class |
filename |
File containing the SNV annotations, where the first column contains the SNV position and the second the chromosome. |
Implementation in R.
object of class IBDsegmentList
in which the annotation for the
tagSNVs is set.
Sepp Hochreiter
S. Hochreiter et al., ‘FABIA: Factor Analysis for Bicluster Acquisition’, Bioinformatics 26(12):1520-1527, 2010.
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
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)