makeBiasBins {chromVAR} | R Documentation

## makeBiasBins

### 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)

[Package chromVAR version 1.4.1 Index]