cexor {CexoR} | R Documentation

## ChIP-exo peak-pair calling with replicates

### Description

ChIP-exo peak-pair calling with replicates.

### Usage

    cexor(bam, chrN, chrL, p=1e-9, dpeaks=c(0,150), dpairs=100, idr=0.01,
    N=5e6, bedfile=TRUE, mu=2.6, sigma=1.3, rho=0.8, prop=0.7)

### Arguments

`bam` | BAM alignment files of biological replicates.
`chrN` | Vector of chromosome names.
`chrL` | Vector of chromosome sizes (bp).
`p` | P-value cutoff (should be relaxed, e.g. 1e-3, to allow the correct estimation of the irreproducible discovery rate (idr). However, this depends on the sequencing depth. For datasets with high number of tag counts, 1e-9 can be appropriate. See the vignette for more information.)
`dpeaks` | Min. and max. allowed distance between peak pairs located at opposed strands in a replicate (bp).
`dpairs` | Max. allowable distance between peak-pair centres across replicates (bp).
`idr` | Irreproducible discovery rate cutoff [0-1].
`N` | Genome is divided in blocks of N bp. for processing. N must be not higher than the size of the smallest chromosome.
`bedfile` | Generate BED files of ChIP-exo reproducible peak pairs.
`mu` | A starting value for the mean of the reproducible component (see 'idr' package).
`sigma` | A starting value for the standard deviation of the reproducible component (see 'idr' package).
`rho` | A starting value for the correlation coefficient of the reproducible component (see 'idr' package).
`prop` | A starting value for the proportion of reproducible component (see 'idr' package).

### Details

Strand specific peak-pair calling in ChIP-exo replicates. The cumulative Skellam distribution function (package 'skellam') is used to detect significant normalized count differences of opposed sign at each DNA strand (peak-pairs). Irreproducible discovery rate for overlapping peak-pairs across biological replicates is estimated using the package 'idr'. The internal functions `pskellam` and `pskellam.sp` from the Jerry W. Lewis' 'skellam' R package (version 0.0-8-7) are used to calculate the cumulative Skellam distribution (see LICENSE file).

### Value

A list containing the following elements:

`bindingEvents` | A GRanges object with reproducible peak pair locations. The metadata 'value' indicates the Irreproducible discovery rate (IDR) estimated at this region, while 'repI.neg.log10pvalue' indicates -log10(p-value) for the replicate I. 'Stouffer.pvalue' and 'Fisher.pvalue' report the combined p-value considering they come from from independent significance tests.
`bindingCentres` | A GRanges object with centre position of reproducible peak pair locations. The metadata 'value' indicates the Irreproducible discovery rate (IDR) estimated at this region, while 'repI.neg.log10pvalue' indicates -log10(p-value) for the replicate I. 'Stouffer.pvalue' and 'Fisher.pvalue' report the combined p-value considering they come from from independent significance tests.
`pairedPeaksRepl` | A GRangesList object with the location of peak pairs retrieved at each replicate. The metadata 'score' indicates -log10(p-value).

### 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 1.26.0 Index]