pcaBeforeCorrection: PCA before correction.

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

PCA before correction.

Usage

pcaBeforeCorrection(rs1, grps, cGsub, batchCL, Conf, type, Ys, theme)

Arguments

rs1	Results of PCA.
grps	Number of batches.
cGsub	Colors
batchCL	A vector identifying batches.
Conf	A vector identifying biological classes.
type	Names biological classes.
Ys	Expression data.
theme	ggplot theme

Details

PCA before correction

Value

Results in the pcaBeforeCorrection 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.