assessComBat: Assessing ComBat corrected data

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 ComBat batch correction.

Usage

assessComBat(rerun1, qopt, nt, rerun12, theme)

Arguments

rerun1	Results of running findBATCH to assess batch effect.
qopt	Optimal number of PCs
nt	Number of biological classes.
rerun12	Results of running findBATCH to assess biological effect.
theme	ggplot theme

Details

Assess if batch effect still exists after ComBat batch correction.

Value

Results in assessComBat 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.

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