| filterPeaks {chromVAR} | R Documentation |
function to get indices of peaks that pass filters
filterPeaks(object, min_fragments_per_peak = 1, non_overlapping = TRUE, ix_return = FALSE)
object |
SummarizedExperiment with matrix of fragment counts per peak
per sample, as computed by |
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 |
if non_overlapping is set to true, when peaks overlap the overlapping peak with lower counts is removed
vector of indices, representing peaks that should be kept
Alicia Schep
getPeaks, filterSamples,
getCounts
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)