mast_filter: Filter a SingleCellAssay
In MAST: Model-based Analysis of Single Cell Transcriptomics

Description Usage Arguments Details Value Functions Author(s) See Also Examples

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

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

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

`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.

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.

A filtered result

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

Andrew McDavid

burdenOfFiltering

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')