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 1.6.7 Index]