makePermutedSets: makePermutedSets

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

Description

Makes annotations sets with similar bias to input sets

Usage

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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)

Author(s)

Alicia Schep

Examples

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# 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)

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