assignPrelim: Single-cell debarcoding (1)

In HelenaLC/CATALYST: Cytometry dATa anALYSis Tools

Single-cell debarcoding (1)

Description

Assigns a preliminary barcode ID to each event.

Usage

assignPrelim(x, bc_key, assay = "exprs", verbose = TRUE)

Arguments

x	a SingleCellExperiment.
bc_key	the debarcoding scheme. A binary matrix with sample names as row names and numeric masses as column names OR a vector of numeric masses corresponding to barcode channels. When the latter is supplied, 'assignPrelim' will create a scheme of the appropriate format internally.
assay	character string specifying which assay to use.
verbose	logical. Should extra information on progress be reported?

Value

a SingleCellExperiment structured as follows:

assays

• counts - raw counts

• exprs - arcsinh-transformed counts

• scaled - population-wise scaled expression using (95%)-quantiles as boundaries

colData

• bc_id - numeric vector of barcode assignments

• delta - separation between positive and negative barcode populations

metadata

• bc_key - the input debarcoding scheme

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

data(sample_ff, sample_key)
sce <- prepData(sample_ff)
sce <- assignPrelim(sce, sample_key)
table(sce$bc_id)

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