makeBiasBins: makeBiasBins

Description Usage Arguments Details Value Methods (by class) Author(s) Examples

Description

Makes bins based on fragment counts

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
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)

Author(s)

Alicia Schep

Examples

1
2
3
# 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.