cexor: ChIP-exo peak-pair calling with replicates

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

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, [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.