Get filter for total umis per barcode based on log transformed values outside (either above, below, or both based on type parameter) nmads median absolute deviations from the median

Source: R/filter_gex_outliers.R

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

filter_total_umi(sce, nmads, type, column = "total_umi")

Arguments

sce

SingleCellExperiment object
nmads

number of median absolute deviations from the median for cutoff
type

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

column in colData containing total UMI count

Value

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

Examples

NULL
#> NULL