filterPeaks {chromVAR} | R Documentation

## filterPeaks

### Description

function to get indices of peaks that pass filters

### Usage

    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

    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)

[Package chromVAR version 1.9.0 Index]