plotcexor {CexoR} | R Documentation

## 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, bioinformatics.engineer@gmail.com

### 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)

[Package CexoR version 1.24.0 Index]