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

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

Contains R scripts for performing formal statistical tests to detect batch effect in genomic datasets, and correct for batch effect using an approach detailed in Nyamundanda et al (2016).

Details

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Explore batch effect (exploBATCH) is an R package for perfoming formal statistical tests to discover batch effect and coorect for it. 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 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., Poudel, P., Patil, Y. and Sadanandam, A., 2017. A novel and robust statistical method to diagnose and correct batch effects in genomic data.

Examples

# Expression data and batch effect variable is required for this function. The first example in the Nyamundanda et al (2017) manuscript 
# requires the gene expression data for breast cancer samples, named Breast (which is in the exploBATCHbreast package on github), and 
# variable identifying batches named batchBreast (in the exploBATCH package) 
require(devtools)
install_github("gnyamundanda/exploBATCHbreast") # install_github requires devtools package
require(exploBATCHbreast)
data(Breast)
data(batchBreast)
expBATCH(D=Breast,batchCL=batchBreast,Conf=NA,mindim=2,maxdim=9,method="ppcca",SDselect=2)

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