getBackgroundPeaks: getBackgroundPeaks

In GreenleafLab/chromVAR: Chromatin Variation Across Regions

Description

Function to get a set of background peaks for each peak based on GC content and # of fragments across all samples

Usage

getBackgroundPeaks(object, ...)

## S4 method for signature 'SummarizedExperiment'
getBackgroundPeaks(object,
  bias = rowData(object)$bias, niterations = 50, w = 0.1, bs = 50)

## S4 method for signature 'RangedSummarizedExperiment'
getBackgroundPeaks(object,
  bias = rowRanges(object)$bias, niterations = 50, w = 0.1, bs = 50)

## S4 method for signature 'MatrixOrmatrix'
getBackgroundPeaks(object, bias, niterations = 50,
  w = 0.1, bs = 50)

Arguments

object	fragment counts as SummarizedExperiment, RangedSummarized, Matrix, or matrix
...	addtional arguments
bias	vector of values for some bias signal for each row of object
niterations	number of background peaks to sample
w	parameter controlling similarity of background peaks
bs	bin size parameter

Details

Background peaks are chosen by sampling peaks based on similarity in GC content and # of fragments across samples using the Mahalanobis distance. The w paramter controls how similar background peaks should be. The bs parameter controls the precision with which the similarity is computed; increasing bs will make the function run slower. Sensible default parameters are chosen for both.

Value

matrix with one row per peak and one column per iteration. values in a row represent indices of background peaks for the peak with that index

Methods (by class)

• SummarizedExperiment: method for SummarizedExperiment

• RangedSummarizedExperiment: method for RangedSummarizedExperiment

• MatrixOrmatrix: method for Matrix or matrix

Examples

# Load very small example counts (already filtered)
data(mini_counts, package = "chromVAR")

# get background peaks
bgpeaks <- getBackgroundPeaks(mini_counts)

GreenleafLab/chromVAR documentation built on Aug. 20, 2019, 11:39 a.m.