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 1.8.6 Index]