filterSamplesPlot {chromVAR} | R Documentation |
plot filtering of samples
filterSamplesPlot(object, min_in_peaks = NULL, min_depth = NULL, use_plotly = interactive())
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 |
use_plotly |
make interactive plot? |
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) counts_filtered_plot <- filterSamplesPlot(counts_filtered, min_in_peaks = 0.15, min_depth = 1500, use_plotly = FALSE)