ppccaBeforeCorrection: PPCCA before correction.

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

Description

PPCCA before correction.

Usage

ppccaBeforeCorrection(res1, grps, cGsub, batchCL, Conf, type, Ys, theme)

Arguments

res1	Results of PPCCA.
grps	Number of batches.
cGsub	Colors
batchCL	A vector identifying batches.
Conf	A vector identifying biological classes.
type	Names of biological classes.
Ys	Expression data
theme	ggplot theme

Details

PPCCA before correction to assess the optimal number of PCs using BIC.

Value

Results in ppccaBeforeCorrection 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.

syspremed/exploBATCH documentation built on May 23, 2019, 9:34 a.m.