filterSamples {chromVAR} | R Documentation

## filterSamples

### Description

function to get indices of samples that pass filtters

### Usage

    filterSamples(object, min_in_peaks = NULL, min_depth = NULL,
      shiny = interactive(), ix_return = FALSE)

### Arguments

`object` | SummarizedExperiment with matrix of fragment counts per peak per sample, as computed by `getCounts`
`min_in_peaks` | minimum fraction of samples within peaks
`min_depth` | minimum library size
`shiny` | make shiny gadget?
`ix_return` | return indices of sample to keep instead of subsetted counts object

### Details

If unspecified, min_in_peaks and min_depth cutoffs will be estimated based on data. min_in_peaks is set to 0.5 times the median proportion of fragments in peaks. min_depth is set to the maximum of 500 or 10 median library size.

### Value

indices of samples to keep

### See Also

`getCounts`, `getPeaks`, `filterPeaks`

### Examples

    data(example_counts, package = "chromVAR")

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

[Package chromVAR version 1.9.0 Index]