findBATCH: A function to formally tests presence of batch effect.
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
Usage
Arguments
Details
Author(s)
References
Description
It searches for directions in the principal subspace that are associated with the batch variable.
Usage
1
findBATCH(res2, qopt, nt, rerun, theme)
Arguments
res2
Results of running findBATCH to assess batch effect.
qopt
Optimal number of PCs
nt
Number of biological classes.
rerun
Results of running findBATCH to assess biological effect.
theme
ggplot theme
Details
It searches for directions in the principal subspace that are associated with the batch variable.
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.
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Description Usage Arguments Details Author(s) References
Description
It searches for directions in the principal subspace that are associated with the batch variable.
Usage
1 | findBATCH(res2, qopt, nt, rerun, theme)
|
Arguments
res2 |
Results of running findBATCH to assess batch effect. |
qopt |
Optimal number of PCs |
nt |
Number of biological classes. |
rerun |
Results of running findBATCH to assess biological effect. |
theme |
ggplot theme |
Details
It searches for directions in the principal subspace that are associated with the batch variable.
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.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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