regionStats: Counts the Windows in Regions of Interest

In MatthiasLienhard/qsea: IP-seq data analysis and vizualization

Counts the Windows in Regions of Interest

Description

This function takes a list of window indices and a list of ROIs and counts the number of overlapping windows

Usage

regionStats(qs, subsets = list(covered = which(rowSums(getCounts(qs)) >= 20)),
 ROIs = list(), minoverlap = 0, maxgap = -1)

Arguments

qs	A qsea Set object
subsets	A list of window indices
ROIs	A list of Regions of Interest
minoverlap	Passed to findOverlaps
maxgap	Passed to findOverlaps

Value

a matrix, containing the total number of windows overlapping the ROIs and the numbers of windows from the subset list overlapping ROIs

Author(s)

Mathias Lienhard

See Also

findOverlaps

Examples

qs=getExampleQseaSet()
#as an example, we analyze the fraction of reads covered by at least 10
#or at least 20 reads, for bins of CpG density
ROIs=list()
regs=getRegions(qs)
cpg=getRegions(qs)$CpG_density
bins=seq(0,30,5)
for(i in 1:(length(bins)-1)){
    n=paste0(bins[i],"-",bins[i+1]," CpGs")
    ROIs[[n]]=regs[which(cpg>=bins[i] & cpg < bins[i+1])]
}
subsets = list(
    ">10" = which(rowSums(getCounts(qs)) >= 10),
    ">20" = which(rowSums(getCounts(qs)) >= 20))
coverage_stats=regionStats(qs, subsets, ROIs)
coverage_stats_rel=coverage_stats[,-1]/coverage_stats[,1]
x=barplot(t(coverage_stats_rel)*100,ylab="fraction of windows[%]",
    beside=TRUE, legend=TRUE, las=2, args.legend=list(x="topleft"), 
    main="Covered Windows")

MatthiasLienhard/qsea documentation built on March 22, 2023, 1:15 p.m.