unionMaxScore-methods: GRanges method to perform union of peaks keeping the score of...

In kamalfartiyal84/compEpiTools: Tools for computational epigenomics

Description

the union between two GRanges associated to scores is performed, and the most significant score for the overlapping regions is returned

Methods

To be used in this form:

unionMaxScore(gr1, gr2, score1=mcols(gr1)[,1], score2=mcols(gr2)[,1])

where:

• gr1: GRanges

• gr2: GRanges

• score1: numeric; the scores (or any kind of score) associated to gr1

• score2: numeric; the scores (or any kind of score) associated to gr2

The method returns the union GRanges as in union(gr1, g2). For each range, if it resulted from overlapping ranges, the maximum score for those ranges is returned. In case pvalues (P) are adopted, they should be transformed in a score with something like -log10(P)

Examples

	gr1 <- GRanges(Rle(c('chr1','chr1')), 
		ranges=IRanges(start=c(100,200), end=c(150,250)), pvalue=c(200, 100))
	gr2 <- GRanges(Rle(c('chr1','chr1')), 
		ranges=IRanges(start=c(80,400), end=c(300,500)), pvalue=c(50, 150))
	unionMaxScore(gr1, gr2)

kamalfartiyal84/compEpiTools documentation built on May 29, 2019, 5:40 a.m.