bindWidth: ChIP-seq Binding Width And Peak Window Size Estimation

In gcapc: GC Aware Peak Caller

Description

ChIP-seq experiments usually use crosslinking strategy to capture sequencing fragments. The fragment location is affected by at least but not limited to two factors, protein real binding and crosslinking operation. This function estimate size of binding part in crosslinked DNA-protein complexes, and denoted that as ChIP-seq binding width.Also, the peak detection window half size is estimated based on binding width.

Usage

bindWidth(coverage, range = c(50L, 500L), step = 50L, odd = TRUE)

Arguments

coverage	A list object returned by function read5endCoverage.
range	A non-nagative integer vector with length 2. This vector set the range within which binding width and peak window size are estimated. Default c(50,500) represents most ChIP-seq experiments.
step	A non-negative integer to set the resolution of binding width estimation within range. This value will be tuned if auto is TRUE. Default 50 is based on default value of range.
odd	A logical vector which, when TRUE, only allows return odd number of binding width, which is preferred by the effective GC content estimation. Default: TRUE.

Value

A numeric vector with 2 elements: Estimated binding width and half size of peak detection window.

Examples

bam <- system.file("extdata", "chipseq.bam", package="gcapc")
cov <- read5endCoverage(bam)
bindWidth(cov)

gcapc documentation built on Nov. 8, 2020, 8:14 p.m.