normCytof {CATALYST} | R Documentation

## Bead-based normalization

### Description

an implementation of Finck et al.'s normalization of mass cytometry data using bead standards with automated bead gating.

### Usage

    normCytof(x, y, ...)

    ## S4 method for signature 'flowFrame'
    normCytof(x, y, out_path = NULL, fn = NULL,
      fn_sep = "_", remove_beads = TRUE, norm_to = NULL, k = 500,
      trim = 5, verbose = TRUE, plot = TRUE)

    ## S4 method for signature 'character'
    normCytof(x, y, out_path = NULL,
      remove_beads = TRUE, norm_to = NULL, k = 500, trim = 5,
      verbose = TRUE)

### Arguments

`x` | a `flowFrame` or character of the FCS file to be normalized.
`y` | `"dvs"` (for bead masses 140, 151, 153, 165, 175) or `"beta"` (for bead masses 139, 141, 159, 169, 175) or a numeric vector of masses.
`...` | optional arguments.
`out_path` | a character string. If specified, outputs will be generated here. If NULL (the default), `normCytof` will return a `flowFrame` of the normalized data (if `remove=FALSE`) or a `flowSet` containing normalized cells and beads (if `remove=TRUE`).
`fn` | a character string to use as the output file name. Defaults to the file name of the input FCS file or `flowFrame`, respectively.
`fn_sep` | a character string to use to separate the output file name's prefix from the appendage.
`remove_beads` | logical. If TRUE (the default) beads will be removed and normalized cells and beads returned separately.
`norm_to` | a `flowFrame` or character of an FCS file from which baseline values should be computed and to which the input data should be normalized.
`k` | integer width of the median window used for bead smoothing.
`trim` | a single non-negative numeric. A median +/- ... mad rule is applied to the preliminary population of bead events to remove bead-bead doublets and low signal beads prior to estimating normalization factors.
`verbose` | logical. Should extra information on progress be reported?
`plot` | logical. Should bead vs. DNA scatters and beads before vs. after normalization be plotted?

### Value

if `out_path=NULL` (the default) a `flowFrame` of the normalized data (if `remove=FALSE`) or `flowSet` containing normalized cells and beads (if `remove=TRUE`). Else, a character of the location where output FCS files and plots have been generated.

### Author(s)

Helena Lucia Crowell helena.crowell@uzh.ch

### References

Finck, R. et al. (2013). Normalization of mass cytometry data with bead standards. Cytometry A 83A, 483-494.

### Examples

    data(raw_data)
    ff <- concatFCS(raw_data)
    normCytof(x = ff, y = "dvs", k = 120)

[Package CATALYST version 1.8.7 Index]