filterSamples {chromVAR} | R Documentation |
function to get indices of samples that pass filtters
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 |
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)