Package 'CexoR'

An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates

Description

Strand specific peak-pair calling in ChIP-exo replicates. The cumulative Skellam distribution function (package 'skellam') is used to detect significant normalised 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'.

Details

Package:	CexoR
Type:	Package
Version:	1.35.1
Date:	2022-05-28
License:	Artistic-2.0 | GPL-2 + file LICENSE
LazyLoad:	yes

Author(s)

Pedro Madrigal,

Maintainer: Pedro Madrigal [email protected]

References

Madrigal P (2015) CexoR: an R/Bioconductor package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates. EMBnet.journal 21: e837.
Skellam JG (1946) The frequency distribution of the difference between two Poisson variates belonging to different populations. J R Stat Soc Ser A 109: 296.
Li Q, Brown J, Huang H, Bickel P (2011) Measuring reproducibility of high-throughput experiments. Ann Appl Stat 5: 1752-1779.
Rhee HS, Pugh BF (2011) Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell 147: 1408-1419.

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 )

---

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, [email protected]

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)

---

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, [email protected]

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)

---