normalizePeaks {chromswitch} | R 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"))

[Package chromswitch version 1.2.1 Index]