correctBatchCYT {CytoTree} | R Documentation |
Remove batch effect in CYT object
correctBatchCYT( object, batch = NULL, par.prior = TRUE, mean.only = TRUE, verbose = FALSE, ... )
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 |
A CYT object with corrected batch effects
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)