filter: Filter a SingleCellAssay

Description

Remove, or flag wells that are outliers in discrete or continuous space.

Usage

filter(sc, groups = NULL, filt_control = NULL, apply_filter = TRUE)

Arguments

The SingleCellAssay object

groups

An optional character naming the grouping variable

filt_control

The list with configuration parameters for the filter.

apply_filter

logical should the filter be applied, or should a matrix of booleans giving if a well would be subject to a filtering criteria be returned?

Value

A filtered result

Details

The function filters wells that don't pass filtering criteria described in filt_control. filt_control is a list with named elements nOutlier (minimum nmber of outlier cells for a cell to be filtered [default = 2] sigmaContinuous (the z-score outlier threshold for the continuous part of the signal) [default = 7] and sigmaProportion (the z-score outlier threshold for the discrete part of the signal) [default = 7].

If groups is provided, the filtering is calculated within each level of the group, then combined again as output.

Examples

Run this code

# NOT RUN {
data(vbetaFA)
## Split by 'ncells', apply to each component, then recombine
vbeta.filtered <- filter(vbetaFA, groups='ncells')
## Returned as boolean matrix
was.filtered <- filter(vbetaFA, apply_filter=FALSE)
## Wells filtered for being discrete outliers
head(subset(was.filtered, pctout))
# }