applyCutoffs {CATALYST} | R Documentation

## Single-cell debarcoding (2)

### Description

Applies separation and mahalanobies distance cutoffs.

### Usage

    applyCutoffs(x, ...)

    ## S4 method for signature 'dbFrame'
    applyCutoffs(x, mhl_cutoff = 30, sep_cutoffs = NULL)

### Arguments

`x` | a `dbFrame`.
`...` | optional arguments.
`mhl_cutoff` | mahalanobis distance threshold above which events should be unassigned. This argument will be ignored if the `mhl_cutoff` slot of the input `dbFrame` is specified.
`sep_cutoffs` | non-negative numeric of length one or of same length as the number of rows in the `bc_key(x)`. Specifies the distance separation cutoffs between positive and negative barcode populations below which events should be unassigned. If `NULL` (default), `applyCutoffs` will try to access the `sep_cutoffs` slot of the input `dbFrame`.

### Value

Will update the `bc_ids` and, if not already specified, `sep_cutoffs` & `mhl_cutoff` slots of `x`.

### Author(s)

Helena Lucia Crowell helena.crowell@uzh.ch

### References

Zunder, E.R. et al. (2015). Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm. Nature Protocols 10, 316-333.

### Examples

    data(sample_ff, sample_key)
    re <- assignPrelim(x = sample_ff, y = sample_key)

    # use global separation cutoff
    applyCutoffs(x = re, sep_cutoffs = 0.4)

    # estimate population-specific cutoffs
    re <- estCutoffs(x = re)
    applyCutoffs(x = re)

[Package CATALYST version 1.10.3 Index]