correctBatchCYT: correctBatchCYT

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

Description

Remove batch effect in CYT object

Usage

correctBatchCYT(
  object,
  batch = NULL,
  par.prior = TRUE,
  mean.only = TRUE,
  verbose = FALSE,
  ...
)

Arguments

object	a CYT object
batch	vector. Batch covariate (only one batch allowed)
par.prior	logical. TRUE indicates parametric adjustments will be used, FALSE indicates non-parametric adjustments will be used.
mean.only	logical. FALSE If TRUE ComBat only corrects the mean of the batch effect (no scale adjustment)
verbose	logical. Whether to show log information
...	Parameters passing to ComBat function

Value

A CYT object with corrected batch effects

See Also

findKNN

Examples

cyt.file <- system.file("extdata/cyt.rds", package = "CytoTree")
cyt <- readRDS(file = cyt.file)
plot.meta <- fetchPlotMeta(cyt)
batch <- as.numeric(plot.meta$stage)
cyt <- correctBatchCYT(cyt, batch = batch)

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