correctBatch: Batch correction approach based on the PPCCA model.

In gnyamundanda/exploBATCH: Explore batch effect (exploBATCH) is a package for discovering and correcting for batch effect using an approach in Nyamundanda et al (2017).

Description

Batch effect is corrected by subtracting its effect in the affected dimensions or PCs. Both corrected and uncorrected dimensions are then used to predict the data.

Usage

correctBatch(res11, designX, Ys, batchCL, ngrps, grps, Conf, nt, cGsub, comres, theme, type)

Arguments

res11	Results of fitting the PPCCA model.
designX	Design matrix for the covariates
Ys	Expression data
batchCL	A vector identifying batches.
ngrps	Number of batches
grps	Batches
Conf	A vector identifying biological classes.
nt	Number of biological classes
cGsub	Colors
comres	Results of ComBat correction
theme	ggplot theme
type	Plot

Details

Batch effect is corrected by subtracting its effect only in the affected dimensions or PCs. Both the corrected and uncorrected dimensions are then used to predict the data.

Value

Results in correctBatch folder in the working directory.

Author(s)

Nyamundanda, G., Poudel, P., Patil, Y. and Sadanandam, A.

References

Nyamundanda, G., Poudel, P., Patil, Y. and Sadanandam, A., 2017. A novel and robust statistical method to diagnose and correct batch effects in genomic data.

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

gnyamundanda/exploBATCH documentation built on May 20, 2019, 3:31 p.m.