Get filter for percentage of mitochondrial reads expressed per barcode

Source: R/filter_gex_outliers.R

Wrapper around scater::isOutlier, arguments type and nmads refer to the same thing. For mitochondrial reads, uses non-log transformed values for deciding cutoffs.

filter_pct_mito(sce, nmads, type, column = "pct_mito")

Arguments

sce

SingleCellExperiment object
nmads

number of median absolute deviations from the median
type

either "both", "lower", or "higher", referring to which side to filter on
column

column in colData containing percentage of mitochondrial reads

Value

Boolean filter with TRUE for cells and FALSE for outliers. Contains attribute with number of median absolute deviations specified.

Details

Ensure that add_pct_gene has been run before this or that a column named pct_mito is present in colData(sce)

Examples

NULL
#> NULL