filterPeaks: filterPeaks

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/filtering.R

Description

function to get indices of peaks that pass filters

Usage

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filterPeaks(object, min_fragments_per_peak = 1, non_overlapping = TRUE,
  ix_return = FALSE)

Arguments

object

SummarizedExperiment with matrix of fragment counts per peak per sample, as computed by getCounts

min_fragments_per_peak

minimum number of fragmints in peaks across all samples

non_overlapping

reduce peak set to non-overlapping peaks, see details

ix_return

return indices of peaks to keep instead of subsetted counts object

Details

if non_overlapping is set to true, when peaks overlap the overlapping peak with lower counts is removed

Value

vector of indices, representing peaks that should be kept

Author(s)

Alicia Schep

See Also

getPeaks, filterSamples, getCounts

Examples

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data(example_counts, package = "chromVAR")

counts_filtered <- filterSamples(example_counts, min_depth = 1500,
                                  min_in_peaks = 0.15, shiny = FALSE)
counts_filtered <- filterPeaks(example_counts)

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