mast_filter: Filter a SingleCellAssay

In RGLab/MAST: Model-based Analysis of Single Cell Transcriptomics

Filter a SingleCellAssay

Description

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

Usage

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

burdenOfFiltering(sc, groups, byGroup = FALSE, filt_control = NULL)

Arguments

sc	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?
byGroup	in the case of burdenOfFiltering should the filter be stratified by groups, or only the plotting.

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.

Value

A filtered result

Functions

• burdenOfFiltering(): plot the proportions of wells are filtered due to different criteria

Author(s)

Andrew McDavid

See Also

burdenOfFiltering

Examples

data(vbetaFA)
## Split by 'ncells', apply to each component, then recombine
vbeta.filtered <- mast_filter(vbetaFA, groups='ncells')
## Returned as boolean matrix
was.filtered <- mast_filter(vbetaFA, apply_filter=FALSE)
## Wells filtered for being discrete outliers
head(subset(was.filtered, pctout))
burdenOfFiltering(vbetaFA, groups='ncells', byGroup=TRUE)
burdenOfFiltering(vbetaFA, groups='ncells')

RGLab/MAST documentation built on Sept. 30, 2023, 1:08 p.m.