get5primeCuts: get the 5' cut sites from a GAlignmentPairs (usually of an...

In RamsinghLab/ATACseeker: Utilities for ATACseq QC, differential accessibility, and integration

Description

get the 5' cut sites from a GAlignmentPairs (usually of an ATAC BAM)

Usage

get5primeCuts(galp, maxSize = 1000, shrink = TRUE, shrinkBy = NULL, ...)

Arguments

galp	a GAlignmentPairs object
maxSize	maximum insert size (for fragmentLengths(galp))
shrink	move the reads around like in the original paper? (TRUE)
shrinkBy	shrink by how much? (realistically this is pointless...)

Value

the 5' ends, from getEnds()

Examples

library(Homo.sapiens)
CUX1_EGID <- org.Hs.egSYMBOL2EG[['CUX1']]
CUX1 <- reduce(transcriptsBy(Homo.sapiens, 'gene')[[CUX1_EGID]])
CUX1bump <- GRanges('chr7', IRanges(101499132, 101501052), '+')

RamsinghLab/ATACseeker documentation built on May 8, 2019, 8:05 a.m.