bindWidth {gcapc} | R Documentation

## ChIP-seq Binding Width And Peak Window Size Estimation

### 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)

[Package gcapc version 1.12.0 Index]