assignPrelim {CATALYST}R Documentation

Single-cell debarcoding (1)

Description

Assigns a preliminary barcode ID to each event.

Usage

assignPrelim(x, y, ...)

## S4 method for signature 'flowFrame,data.frame'
assignPrelim(x, y, cofactor = 10,
  verbose = TRUE)

## S4 method for signature 'flowFrame,vector'
assignPrelim(x, y, cofactor = 10,
  verbose = TRUE)

## S4 method for signature 'character,data.frame'
assignPrelim(x, y, cofactor = 10,
  verbose = TRUE)

## S4 method for signature 'character,vector'
assignPrelim(x, y, cofactor = 10,
  verbose = TRUE)

Arguments

x

a flowFrame or character of an FCS file name.

y

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.

...

optional arguments.

cofactor

numeric. Cofactor used for asinh transformation.

verbose

logical. Should extra information on progress be reported?

Value

Returns a dbFrame containing measurement intensities, the debarcoding key, a numeric verctor of barcode IDs and separations between positive and negative barcode populations, and barcode intensities normalized by population.

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)
assignPrelim(x = sample_ff, y = sample_key)


[Package CATALYST version 1.8.7 Index]