range_summary: Get the signal from bigwig file for defined regions.

In SamBuckberry/RunATAC: Functions for Importing, Processing, Analyzing, Plotting and Reformatting ATAC-seq Data

Description

Get the signal from bigwig file for defined regions.

Usage

range_summary(bigwig, gr, range = 100, log = FALSE, aggregate = FALSE)

Arguments

bigwig	Path to a bigwig file. Also accpets http paths.
gr	A genomic ranges object of regions to obtain signal. All ranges should be the same width.
range	The distance from the centre of gr to flank. Default=100.
log	Logical. Is the signal in the bigwig file in log space? Default=FALSE. If log = TRUE, the scores in the bigwig file are transformed by e^scores.
aggregate	Logical. Should data for each position be added to get an aggregate score?

Value

A numeric vector of aggregate signal if aggregate = TRUE, which is the default. If aggregate = FALSE a data.frame of signal of all regions is returned.

SamBuckberry/RunATAC documentation built on Aug. 2, 2021, 9:54 a.m.