makePermutedSets

Makes annotations sets with similar bias to input sets

makePermutedSets(object, annotations, ...)

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


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

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

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

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

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

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

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

# S4 method for 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

Value

SummarizedExperiment storing bias bins annotation

Details

Will create nbins * 3 annotations based on sampling from peaks with a certain fragment count, fragment count, or fragment count & bias.

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

Examples

# NOT RUN {
# 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)
# }