applyCutoffs: Single-cell debarcoding (2)

In HelenaLC/CATALYST: Cytometry dATa anALYSis Tools

Single-cell debarcoding (2)

Description

Applies separation and mahalanobies distance cutoffs.

Usage

applyCutoffs(x, assay = "exprs", mhl_cutoff = 30, sep_cutoffs = NULL)

Arguments

x	a SingleCellExperiment.
assay	character string specifying which assay data to use. Should be one of assayNames(x) and correspond to expression-like not count data.
mhl_cutoff	numeric mahalanobis distance threshold above which events should be unassigned; ignored if metadata(x)$mhl_cutoff exists.
sep_cutoffs	non-negative numeric of length one or of same length as the number of rows in the bc_key(x). Specifies the distance separation cutoffs between positive and negative barcode populations below which events should be unassigned. If NULL (default), applyCutoffs will try to access metadata(x)$sep_cutoffs.

Value

the input SingleCellExperiment x is returned with updated colData columns "bc_id" and "mhl_dist", and an additional int_metadata slot "mhl_cutoff" containing the applied mahalanobies distance cutoff.

Author(s)

Helena L Crowell [e-mail]

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

library(SingleCellExperiment)

# construct SCE
data(sample_ff, sample_key)
sce <- prepData(sample_ff)
    
# assign preliminary barcode IDs
# & estimate separation cutoffs
sce <- assignPrelim(sce, sample_key)
sce <- estCutoffs(sce)

# use estimated population-specific 
# vs. global separation cutoff(s)
sce1 <- applyCutoffs(sce)
sce2 <- applyCutoffs(sce, sep_cutoffs = 0.35)

# compare yields after applying cutoff(s)
c(global = mean(sce1$bc_id != 0), 
specific = mean(sce2$bc_id != 0))
  

HelenaLC/CATALYST documentation built on Nov. 30, 2024, 4:04 a.m.