mast_filter {MAST} | R Documentation

## 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')

[Package MAST version 1.12.0 Index]