filterPeaks

function to get indices of peaks that pass filters

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

Value

vector of indices, representing peaks that should be kept

Details

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

See also

getPeaks, filterSamples, getCounts

Examples

# NOT RUN {
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)
# }