plotIBDsegment: Plots an IBD segment given genotype data and tagSNVs

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

Description

plotIBDsegment: R implementation of plotIBDsegment.

A IBD segment is plotted where individuals that are plotted must be provided together with tagSNVs and their physical positions. The individuals are provided as genotyping matrix. The model, i.e. the tagSNVs, is shown, too. Annotations of tagSNVs like match with another genome (Neandertal, Denisova) can be visualized.

Usage

plotIBDsegment(Lout,tagSNV,physPos=NULL,colRamp=12,val=c(0.0,2.0,1.0),chrom="",count=0,labelsNA=NULL,prange=NULL,labelsNA1=c("model L"),grid=FALSE,pairs=FALSE,...)

Arguments

Lout	the alleles of the individuals are provided; typically via a previous call of the fabia function readSamplesSpfabia.
tagSNV	tagSNVs given as numbers if all SNVs are enumerated.
physPos	physical position of tagSNVs in bp.
colRamp	passed to matrixPlot: color representation.
val	vector of 3 components containing values for representation of reference allele, minor allele that is not tagSNV, minor allele that is tagSNV, respectively.
chrom	chromosome as string.
count	counter which is shown in the title if larger than 0 (for viewing a series of IBD segments).
labelsNA	labels for the individuals.
prange	vector of two integer values giving the begin and end of a subinterval of the interval for zooming in.
labelsNA1	labels for tagSNVs by the model obtained by fabia; other tagSNV annotations like match with another genome (Neandertal, Denisova) can be visualized.
grid	does the plot have a grid?; default FALSE (no).
pairs	for pairwise groups, e.g. case-control, twins, etc.; default FALSE (no).
...	other graphical parameters may also be passed as arguments to this function.

Details

A IBD segment is plotted showing tagSNVs and minor alleles of other SNVs. Provided are individuals to plot together with tagSNVs and their physical positions. Other annotations of tagSNVs can be visualized.

In the plot the $y$-axis gives the individuals or the chromosomes and the $x$-axis consecutive SNVs. The default color coding uses yellow for major alleles, violet for minor alleles of tagSNVs, and blue for minor alleles of other SNVs. model L indicates tagSNVs identified by hapFabia in violet.

Implementation in R.

Value

Plots an IBD segment given genotype data and tagSNVs

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)

data(simu)

namesL <- simu[["namesL"]]
haploN <- simu[["haploN"]]
snvs <- simu[["snvs"]]
annot <- simu[["annot"]]
alleleIimp <- simu[["alleleIimp"]]
write.table(namesL,file="dataSim1fabia_individuals.txt",
   quote = FALSE,row.names = FALSE,col.names = FALSE)
write(as.integer(haploN),file="dataSim1fabia_annot.txt",
   ncolumns=100)
write(as.integer(snvs),file="dataSim1fabia_annot.txt",
   append=TRUE,ncolumns=100)
write.table(annot,file="dataSim1fabia_annot.txt",
   sep = " ", quote = FALSE,row.names = FALSE,
   col.names = FALSE,append=TRUE)
write(as.integer(haploN),file="dataSim1fabia_mat.txt",
   ncolumns=100)
write(as.integer(snvs),file="dataSim1fabia_mat.txt",
   append=TRUE,ncolumns=100)

for (i in 1:haploN) {

  a1 <- which(alleleIimp[i,]>0.01)

  al <- length(a1)
  b1 <- alleleIimp[i,a1]

  a1 <- a1 - 1
  dim(a1) <- c(1,al)
  b1 <- format(as.double(b1),nsmall=1)
  dim(b1) <- c(1,al)

  write.table(al,file="dataSim1fabia_mat.txt",
     sep = " ", quote = FALSE,row.names = FALSE,
     col.names = FALSE,append=TRUE)
  write.table(a1,file="dataSim1fabia_mat.txt",
     sep = " ", quote = FALSE,row.names = FALSE,
     col.names = FALSE,append=TRUE)
  write.table(b1,file="dataSim1fabia_mat.txt",
     sep = " ", quote = FALSE,row.names = FALSE,
     col.names = FALSE,append=TRUE)

}



mergedIBDsegmentList <- hapRes$mergedIBDsegmentList
individuals <- individuals(mergedIBDsegmentList[[1]])
tagSNVs <- tagSNVs(mergedIBDsegmentList[[1]])
tagSNVs <-
   as.integer(sort.int(as.integer(unique(tagSNVs))))
tagSNVPositions <-
   tagSNVPositions(mergedIBDsegmentList[[1]])
labelIndividuals <-
   labelIndividuals(mergedIBDsegmentList[[1]])
Lout <- readSamplesSpfabia(X="dataSim1fabia_mat",
   samples=individuals,lowerB=0,upperB=1000.0)
tagSNVsL <- list(tagSNVs)
labelsK <- c("model L")
plotIBDsegment(Lout=Lout,tagSNV=tagSNVsL,
   physPos=tagSNVPositions,colRamp=12,val=c(0.0,2.0,1.0),
   chrom="1",count=0,labelsNA=labelIndividuals,
   labelsNA1=labelsK)

setwd(old_dir)

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