normCytof {CATALYST} | R Documentation |
an implementation of Finck et al.'s normalization of mass cytometry data using bead standards with automated bead gating.
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)
x |
a |
y |
|
... |
optional arguments. |
out_path |
a character string. If specified, outputs will be generated here. If NULL
(the default), |
fn |
a character string to use as the output file name. Defaults to
the file name of the input FCS file or |
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 |
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? |
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.
Helena Lucia Crowell helena.crowell@uzh.ch
Finck, R. et al. (2013). Normalization of mass cytometry data with bead standards. Cytometry A 83A, 483-494.
data(raw_data) ff <- concatFCS(raw_data) normCytof(x = ff, y = "dvs", k = 120)