combatMod: Call ComBat function with minor adjustments
In kokrah/cbcbSEQ: RNAseq analysis pipeline for UMD CBCB collaborators with batch effect assessment and correction
Description
Usage
Arguments
Value
Description
It is worth noting that sva's ComBat has some of these modifications now.
Usage
1
2
Arguments
dat
Genomic measure matrix (dimensions probe x sample)
batch
Batch covariate (multiple batches allowed)
mod
bio factor of interest
numCovs
The column numbers of the variables in mod to be treated as continuous variables
noScale
do not adjust scale for batch (use default(TRUE) for now)
prior.plots
(Optional) TRUE gives prior plots. Used only when noScale is FALSE
Value
list containing adjusted data(bayesdata), shift adjustments(gamma.star), and scale adjustments(delta.star)
kokrah/cbcbSEQ documentation built on May 20, 2019, 12:54 p.m.
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Description Usage Arguments Value
Description
It is worth noting that sva's ComBat has some of these modifications now.
Usage
1 2 |
Arguments
dat |
Genomic measure matrix (dimensions probe x sample) |
batch |
Batch covariate (multiple batches allowed) |
mod |
bio factor of interest |
numCovs |
The column numbers of the variables in mod to be treated as continuous variables |
noScale |
do not adjust scale for batch (use default(TRUE) for now) |
prior.plots |
(Optional) TRUE gives prior plots. Used only when noScale is FALSE |
Value
list containing adjusted data(bayesdata), shift adjustments(gamma.star), and scale adjustments(delta.star)
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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