makePermutedSets: makePermutedSets

In chromVAR: Chromatin Variation Across Regions

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)

chromVAR documentation built on Nov. 8, 2020, 6:46 p.m.