runFastPCA: Calculate principal components in CYT

In JhuangLab/CytoTree: A Toolkit for Flow And Mass Cytometry Data

Description

Calculate principal components in CYT

Usage

runFastPCA(object, center = FALSE, scale. = TRUE, verbose = FALSE, ...)

Arguments

object	a CYT object
center	logical, a logical value indicating whether the variables should be shifted to be zero centered. Alternately, a vector of length equal the number of columns of x can be supplied. The value is passed to scale. See fast.prcomp
scale.	logical, a logical value indicating whether the variables should be scaled to have unit variance before the analysis takes place. The default is FALSE for consistency with S, but in general scaling is advisable. Alternatively, a vector of length equal the number of columns of x can be supplied. The value is passed to scale. See fast.prcomp
verbose	logical. Whether to print calculation progress.
...	Parameters passing to fast.prcomp function

Value

A CYT object with PCA

See Also

fast.prcomp

Examples

cyt.file <- system.file("extdata/cyt.rds", package = "CytoTree")
cyt <- readRDS(file = cyt.file)

cyt <- runFastPCA(cyt, verbose = TRUE)

JhuangLab/CytoTree documentation built on Nov. 16, 2020, 7:23 a.m.