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

Description Usage Arguments Details Value See Also Examples

function to get indices of samples that pass filtters

1 2	filterSamples(object, min_in_peaks = NULL, min_depth = NULL, shiny = interactive(), ix_return = FALSE)

`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

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.

indices of samples to keep

getCounts, getPeaks, filterPeaks

        
data(example_counts, package = "chromVAR")

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