convertGRanges2GPos: Convert GRanges with scores to GPos

In CAGEfightR: Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

Description

Converts a GRanges to a GPos, correctly expanding the score column. This is useful is nearby CTSSs with the same count are grouped in the same range (see example).

Usage

convertGRanges2GPos(object)

Arguments

object

GRanges object with a score column

Value

GPos with score column

Examples

# Example GRanges
gr <- GRanges(Rle(c("chr2", "chr2", "chr3", "chr4")),
              IRanges(start=c(1, 10, 5, 3),
              end=c(5L, 10L, 5L, 4L)),
              strand="+",
              score=c(2, 1, 3, 11))

# Expand to proper GPos / CTSS format:
gp <- convertGRanges2GPos(gr)

# Double check that the total number of counts remains the same
stopifnot(sum(score(gr) * width(gr)) == sum(score(gp)))

CAGEfightR documentation built on Nov. 8, 2020, 5:42 p.m.