assessCorrectBATCH: Assessing data corrected for batch effect using correctBATCH.

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

Assess if batch effect still exists after correctBATCH batch correction.

Usage

assessCorrectBATCH(rerun2, qopt, nt, rerun22, theme)

Arguments

rerun2	Results of running findBATCH to assess batch effect.
qopt	Optimal number of PCs.
nt	Number of biological classes.
rerun22	Results of running findBATCH to assess biological effect.
theme	ggplot theme

Details

Assess if batch effect still exists after correctBATCH batch correction.

Value

Results in assessCorrectBATCH 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.