R: makePermutedSets

makePermutedSets {chromVAR}

R Documentation

makePermutedSets

Description

Makes annotations sets with similar bias to input sets

Usage

makePermutedSets(object, annotations, ...)

## S4 method for signature 'SummarizedExperiment,SummarizedExperiment'
makePermutedSets(object,
  annotations, bias = rowData(object)$bias, window = 10)


  ## S4 method for signature 'RangedSummarizedExperiment,SummarizedExperiment'
makePermutedSets(object,
  annotations, bias = rowRanges(object)$bias, window = 10)

## S4 method for signature 'MatrixOrmatrix,SummarizedExperiment'
makePermutedSets(object,
  annotations, bias, window = 10)

## S4 method for signature 'SummarizedExperiment,MatrixOrmatrix'
makePermutedSets(object,
  annotations, bias = rowData(object)$bias, window = 10)

## S4 method for signature 'RangedSummarizedExperiment,MatrixOrmatrix'
makePermutedSets(object,
  annotations, bias = rowRanges(object)$bias, window = 10)

## S4 method for signature 'MatrixOrmatrix,MatrixOrmatrix'
makePermutedSets(object, annotations,
  bias, window = 10)

## S4 method for signature 'SummarizedExperiment,list'
makePermutedSets(object, annotations,
  bias = rowData(object)$bias, window = 10)

## S4 method for signature 'RangedSummarizedExperiment,list'
makePermutedSets(object,
  annotations, bias = rowRanges(object)$bias, window = 10)

## S4 method for signature 'MatrixOrmatrix,list'
makePermutedSets(object, annotations, bias,
  window = 10)

Arguments

`object`	fragment counts stored as RangedSummarizedExperiment, SummarizedExperiment, matrix, or Matrix
`annotations`	annotations as SummarizedExperiment, matrix, or list
`...`	additional arguments
`bias`	vector of some bias signal (usually gc content) for each row of object
`window`	number of nearest neighbors to consider

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)

object = SummarizedExperiment,annotations = SummarizedExperiment: method for SummarizedExperiment and SummarizedExperiment
object = RangedSummarizedExperiment,annotations = SummarizedExperiment: method for RangedSummarizedExperiment and SummarizedExperiment
object = MatrixOrmatrix,annotations = SummarizedExperiment: method for Matrix or matrix and SummarizedExperiment
object = SummarizedExperiment,annotations = MatrixOrmatrix: method for SummarizedExperiment and MatrixOrmatrix
object = RangedSummarizedExperiment,annotations = MatrixOrmatrix: method for RangedSummarizedExperiment and MatrixOrmatrix
object = MatrixOrmatrix,annotations = MatrixOrmatrix: method for Matrix/matrix and Matrix/matrix
object = SummarizedExperiment,annotations = list: method for SummarizedExperiment and list
object = RangedSummarizedExperiment,annotations = list: method for RangedSummarizedExperiment and list
object = MatrixOrmatrix,annotations = list: method for Matrix or matrix and list

Author(s)

Alicia Schep

Examples

# Load very small example counts (already filtered)
data(mini_counts, package = "chromVAR")
data(example_motifs, package = "motifmatchr")
library(motifmatchr)
library(BSgenome.Hsapiens.UCSC.hg19)
motif_ix <- matchMotifs(example_motifs, mini_counts, 
                         genome = BSgenome.Hsapiens.UCSC.hg19)

perm_sets <- makePermutedSets(mini_counts, motif_ix)

[Package chromVAR version 1.9.0 Index]