correctBatchCYT: correctBatchCYT

Description Usage Arguments Value See Also Examples

View source: R/batch.R

Description

Remove batch effect in CYT object

Usage

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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

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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.