CexoR (version 1.10.0)

plotcexor: Visualization of ChIP-exo peak-pair calling with replicates

Description

Visualization of ChIP-exo peak-pair calling with replicates.

Usage

plotcexor(bam, peaks, EXT=500)

Arguments

bam

BAM alignment files of biological replicates.

peaks

Object (list) output of the function 'cexor'.

EXT

Extension (bp) upstream and downstream the central position of reproducible peak pair locations for visulization purposes.

Value

R plot.

Details

Visualization of ChIP-exo peak-pair calling with replicates.

References

Madrigal P (2015) CexoR: an R/Bioconductor package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates. EMBnet.journal 21: e837.

See Also

CexoR-package

Examples

## hg19. chr2:1-1,000,000. CTCF data from Rhee and Pugh (2011)

owd <- setwd(tempdir())

rep1 <- "CTCF_rep1_chr2_1-1e6.bam"
rep2 <- "CTCF_rep2_chr2_1-1e6.bam"
rep3 <- "CTCF_rep3_chr2_1-1e6.bam"
r1 <- system.file("extdata", rep1, package="CexoR",mustWork = TRUE)
r2 <- system.file("extdata", rep2, package="CexoR",mustWork = TRUE)
r3 <- system.file("extdata", rep3, package="CexoR",mustWork = TRUE)

chipexo <- cexor(bam=c(r1,r2,r3), chrN="chr2", chrL=1e6, idr=0.01, p=1e-12, N=3e4)

plotcexor(bam=c(r1,r2,r3), peaks=chipexo, EXT=500)

setwd(owd)