applyGRonGR: Apply a function on a data from gr2 with windows provided by...

In CellFateNucOrg/nanodsmf: Analyse nanopore dual enzyme single molecule footprinting data (nanoDSMF)

Description

Apply a function to summarise data from multiple metadata columns of GRanges in gr2 that fall within GRanges provided by gr1

Usage

applyGRonGR(gr1, gr2, applyTo, fun, ...)

Arguments

gr1	A GenomicRanges object with windows of interest
gr2	A GenomicRanges object with data of interest
applyTo	Vector with names of columns in gr2 on which to apply the function
fun	Function to apply (e.g. sum, mean, paste0)

Value

GRanges from gr1 with summed values of metadata columns from gr2

Examples

# single gr
gr1 <- GenomicRanges::GRanges("chr1", IRanges::IRanges(c(1,3,7), c(5,6,10),names=paste0("win", letters[1:3])), score=4:6)
gr2 <- GenomicRanges::GRanges("chr1", IRanges::IRanges(c(1, 3, 8), c(1, 3, 8),names=paste0("dataID:", letters[1:3])), score=c(10,20,30))
applyGRonGR(gr1,gr2,applyTo="score",fun=sum)
gr1 <- GenomicRanges::GRanges("chr1", IRanges::IRanges(c(1,3,7), c(5,6,10),names=paste0("win", letters[1:3])), score=4:6, other=1:3)
gr2 <- GenomicRanges::GRanges("chr1", IRanges::IRanges(c(1, 3, 8), c(1, 3, 8),names=paste0("dataID:", letters[1:3])), score=c(10,20,30), other=c(100,NA,300))
applyGRonGR(gr1,gr2,c("score","other"),fun=sum,na.rm=T)

CellFateNucOrg/nanodsmf documentation built on July 23, 2020, 4:57 p.m.