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

Description Usage Arguments Value Examples

View source: R/get5primeCuts.R

Description

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

Usage

1
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

1
2
3
4
library(Homo.sapiens)
CUX1_EGID <- org.Hs.egSYMBOL2EG[['CUX1']]
CUX1 <- reduce(transcriptsBy(Homo.sapiens, 'gene')[[CUX1_EGID]])
CUX1bump <- GRanges('chr7', IRanges(101499132, 101501052), '+')

biobenkj/ATACseeker documentation built on May 7, 2019, 8:36 a.m.