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]