filterSamples

function to get indices of samples that pass filtters

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

Value

indices of samples to keep

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.

See also

getCounts, getPeaks, filterPeaks

Examples

# NOT RUN {

data(example_counts, package = "chromVAR")

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