correctBatchFSPY: correctBatchFSPY

In flowSpy: A Toolkit for Flow And Mass Cytometry Data

Description

Remove batch effect in FSPY object

Usage

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

Arguments

object	An FSPY 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

An FSPY object after removing batch effect

An FSPY object with corrected batch effects

See Also

findKNN

Examples

if (FALSE) {
  plot.meta <- fetchPlotMeta(fspy)
  batch <- as.numeric(plot.meta$stage)
  fspy <- correctBatchFSPY(object, batch = batch)
}

flowSpy documentation built on Nov. 8, 2020, 6:53 p.m.