makeBiasBins

Makes bins based on fragment counts

makeBiasBins(object, ...)

# S4 method for SummarizedExperiment
makeBiasBins(object,
  bias = rowData(object)$bias, nbins = 25, frac = 0.3)

# S4 method for RangedSummarizedExperiment
makeBiasBins(object,
  bias = rowRanges(object)$bias, nbins = 25, frac = 0.3)

# S4 method for 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

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)

  • SummarizedExperiment: method for SummarizedExperiment

  • RangedSummarizedExperiment: method for RangedSummarizedExperiment

  • MatrixOrmatrix: method for Matrix or matrix

Examples

# NOT RUN {
# Load very small example counts (already filtered)
data(mini_counts, package = "chromVAR")
bb <- makeBiasBins(mini_counts)
# }