add.broad.peak.regions: Calculate chromosome-wide profiles of smoothed tag density

In spp: ChIP-Seq Processing Pipeline

Description

Looks for broader regions of enrichment associated with the determined peak positions, adds them to the $npl data as $rs, $re columns.

Usage

add.broad.peak.regions(chip.tags,input.tags,bp,window.size=500,z.thr=2)

Arguments

chip.tags	signal chromosome tag coordinate vectors (e.g. output of select.informative.tags
input.tags	optionall control (input) tags
bp	output of find.binding.positions call
window.size	window size to be used in calculating enrichment
z.thr	Z-score corresponding to the Poisson ratio threshold used to flag significantly enriched windows

Value

A structure identical to bp (binding.postions) with two additional columns added (rs and re) corresponding to start and end of the associated significantly enriched region. If no region was associated with a particular peak, NAs values are reported.

spp documentation built on May 30, 2019, 5:03 p.m.