percentileNorm: Percentile Normalization
In buschlab/MBECS: Evaluation and correction of batch effects in microbiome data-sets
Description
Usage
Arguments
Details
Value
Examples
Description
Wrapper to help perform percentile normalization on a matrix of counts.
Takes counts and a data-frame of grouping variables and returns a matrix of
transformed counts. This is designed (by the Developers of the procedure) to
work with case/control experiments by taking the untreated group as reference
and adjusting the other groupings of TRT x Batch to it.
Usage
1
percentileNorm(cnts, meta)
Arguments
cnts
A numeric matrix of abundances (samples x features).
meta
Data-frame of covariate columns, first column contains batches,
second column contains grouping.
Details
The function returns a matrix of normalized abundances.
Value
Numeric matrix of corrected/normalized counts.
Examples
1
2
3
4
# This will return a matrix of normalized counts, according to the covariate
# information in meta
mtx.pn_counts <- percentileNorm(cnts=dummy.list$cnts,
meta=dummy.list$meta[,c("batch","group")])
buschlab/MBECS documentation built on Jan. 21, 2022, 1:27 a.m.
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Description Usage Arguments Details Value Examples
Description
Wrapper to help perform percentile normalization on a matrix of counts. Takes counts and a data-frame of grouping variables and returns a matrix of transformed counts. This is designed (by the Developers of the procedure) to work with case/control experiments by taking the untreated group as reference and adjusting the other groupings of TRT x Batch to it.
Usage
1 | percentileNorm(cnts, meta)
|
Arguments
cnts |
A numeric matrix of abundances (samples x features). |
meta |
Data-frame of covariate columns, first column contains batches, second column contains grouping. |
Details
The function returns a matrix of normalized abundances.
Value
Numeric matrix of corrected/normalized counts.
Examples
1 2 3 4 | # This will return a matrix of normalized counts, according to the covariate
# information in meta
mtx.pn_counts <- percentileNorm(cnts=dummy.list$cnts,
meta=dummy.list$meta[,c("batch","group")])
|
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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