assignPrelim {CATALYST} | R Documentation

## 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_idnumeric verctor of barcode assignments

  - deltaseparation between positive and negative barcode populations

`metadata`

  - bc_keythe input debarcoding scheme

### Author(s)

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

[Package CATALYST version 1.14.1 Index]