filterPeaks: filterPeaks
In GreenleafLab/chromVAR: Chromatin Variation Across Regions

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

function to get indices of peaks that pass filters

1 2	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 `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

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)