filterSamplesPlot: filterSamplesPlot

Description Usage Arguments Details Value See Also Examples

View source: R/filtering.R

Description

plot filtering of samples

Usage

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filterSamplesPlot(object, min_in_peaks = NULL, min_depth = NULL,
  use_plotly = interactive())

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

use_plotly

make interactive plot?

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

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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)

chromVAR documentation built on May 2, 2018, 4:34 a.m.