cexor | R Documentation |
ChIP-exo peak-pair calling with replicates.
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)
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). |
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).
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). |
Pedro Madrigal, pmadrigal@ebi.ac.uk
Madrigal P (2015) CexoR: an R/Bioconductor package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates. EMBnet.journal 21: e837.
CexoR-package
## 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)
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