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

In pmb59/CexoR: An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates

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.

Details

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

Value

R plot.

Author(s)

Pedro Madrigal, [e-mail]

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)

pmb59/CexoR documentation built on May 31, 2022, 4:38 a.m.