normalizePeaks: normalizePeaks

View source: R/global_processing.R

normalizePeaksR Documentation

normalizePeaks

Description

Given a set of peak calls for different marks and samples, normalize all peaks genome-wide for each sample and mark by rescaling and Winsorizing, i.e. rescale the middle of the data to the range [0, 1] and bound the upper tail to 1 and the lower tail to 0, effectively replacing a fixed amount of extreme values in each tail. Similar to trimming the tails except instead of discarding the tails entirely they're bounded.

Usage

normalizePeaks(peaks, columns, tail = 0.005)

Arguments

peaks

List of GRanges objects storing peak calls for each sample, where element names correspond to sample IDs

columns

Character vector specifying the names of columns to normalize

tail

Optional: numeric, a fraction in [0, 1] specifying how much of the data to bound to 0 (for the lower tail) or 1 (for the upper tail). Default: 0.005.

Value

A list of GRanges objects storing peak calls for each sample, with columns specified in columns normalized.

See Also

winsorNorm

Examples

normalizePeaks(H3K4me3, columns = c("signalValue", "pValue", "qValue"))


sjessa/chromswitch documentation built on Feb. 4, 2024, 2:04 a.m.