makeBiasBins: makeBiasBins

In GreenleafLab/chromVAR: Chromatin Variation Across Regions

Description

Makes bins based on fragment counts

Usage

makeBiasBins(object, ...)

## S4 method for signature 'SummarizedExperiment'
makeBiasBins(object,
  bias = rowData(object)$bias, nbins = 25, frac = 0.3)

## S4 method for signature 'RangedSummarizedExperiment'
makeBiasBins(object,
  bias = rowRanges(object)$bias, nbins = 25, frac = 0.3)

## S4 method for signature 'MatrixOrmatrix'
makeBiasBins(object, bias, nbins = 25,
  frac = 0.3)

Arguments

object	fragment counts stored as RangedSummarizedExperiment, SummarizedExperiment, matrix, or Matrix
...	addtional arguments
bias	vector of some bias signal (usually gc content) for each row of object
nbins	number of bins for each category, see Details
frac	fraction of peaks within given bin to select randomly

Details

Will create nbins * 3 annotations based on sampling from peaks with a certain fragment count, fragment count, or fragment count & bias.

Value

SummarizedExperiment storing bias bins annotation

Methods (by class)

• SummarizedExperiment: method for SummarizedExperiment

• RangedSummarizedExperiment: method for RangedSummarizedExperiment

• MatrixOrmatrix: method for Matrix or matrix

Author(s)

Alicia Schep

Examples

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

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