Description Usage Arguments Value See Also Examples
Remove batch effect in CYT object
1 2 3 4 5 6 7 8 |
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
1 2 3 4 5 | 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)
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