exploBATCH-package: Explore batch effect (exploBATCH) is a package for...

In syspremed/exploBATCHSerial: Explore batch effect (exploBATCH) is a package for discovering and correcting for batch effect using an approach in Nyamundanda et al (2016).

Description

It contains R scripts for performing formal statistical tests to diagnose batch effect in large scale genomic datasets, and correct for batch effect using an approach detailed in Nyamundanda et al (2016), which is based on the PPCCA model,in large scale genomic datasets. License: What license is it under?

Details

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Explore batch effect (exploBATCH) is an R package for perfoming formal statistical tests to discover and correct batch effect. It searches for directions in the principal subspace that are associated with the batch variable of interest and correct for batch effect by subtracting this effect only in the affected dimensions. Both the corrected and uncorrected dimensions are then used to predict the data.

Author(s)

Gift Nyamundanda [e-mail]

Maintainer: Gift Nyamundanda <[e-mail]>

References

Nyamundanda, G. and Sadanandam, A., 2016. A novel and robust statistical method to diagnose and correct batch effects in large-scale genomic data.

See Also

~~ Optional links to other man pages, e.g. ~~ ~~ <pkg> ~~

Examples

## help(exploBATCH)
## Expression data and batch effect variable is required for this function.
data(Breast)
data(batchBreast)
expBATCH(D= Breast,batchBreast,Conf=NA,mindim=1,maxdim=10,method="ppcca")

syspremed/exploBATCHSerial documentation built on May 20, 2019, 8:33 a.m.