adjustPeaks: Adjust peak width so that samples obtained under different...

In chroGPS: chroGPS2: Generation, visualization and differential analysis of epigenome maps

Description

Peaks obtained under different conditions (e.g. chip-chip, chip-seq, mnase-seq) are typically not comparable in terms of their width. adjustPeaks modifies the mean and SD of the peak width distribution for each condition, so that they become equivalent to the condition with widest peaks. See details.

Usage

adjustPeaks(x, adjust, sampleid, logscale = TRUE) 

Arguments

x	GRangesList indicating the binding sites for each sample/experiment.
adjust	Vector indicating the adjustment factor, i.e. the condition under which each sample has been obtained.
sampleid	Vector containing the sample identifier. sampleid should take the same value for samples obtained under different conditions, as this is used to detect the samples to be used for Procrustes adjustment.
logscale	If set to TRUE the mean and SD are matched for log width, otherwise the original widths are used. Working in log scale can help reduce the effect of outliers (e.g. an usually long binding site).

Details

In a sense, the peak calling resolution is decreased so that they become comparable to the less precise technology (notice that there is no reliable way to increase the precision given by a low-resolution technology).

Value

GRangesList object with adjusted widths.

Methods

signature(x='GRangesList')

Each element in x contains the binding sites for a different sample. The start, end and chrosomome of each binding sites should be accessed via start, end and space.

See Also

procrustesAdj for an alternative, more general, adjustment based on Procrustes. distGPS for computing distances, mds to create MDS-oriented objects.

Examples

#See examples in help(procrustesAdj)

chroGPS documentation built on Oct. 31, 2019, 4:52 a.m.