PC_correction: Apply Principal Component (PC)-based correction for...
In almeidasilvaf/BioNERO: Biological Network Reconstruction Omnibus
View source: R/data_preprocess.R
PC_correction R Documentation
Apply Principal Component (PC)-based correction for confounding artifacts
Description
Apply Principal Component (PC)-based correction for confounding artifacts
Usage
PC_correction(exp, verbose = FALSE)
Arguments
exp
A gene expression data frame with genes in row names
and samples in column names or a 'SummarizedExperiment' object.
verbose
Logical indicating whether to display progress
messages or not. Default: FALSE.
Value
Corrected expression data frame or 'SummarizedExperiment' object.
Author(s)
Fabricio Almeida-Silva
References
Parsana, P., Ruberman, C., Jaffe, A. E., Schatz, M. C., Battle, A., &
Leek, J. T. (2019). Addressing confounding artifacts in reconstruction of
gene co-expression networks. Genome biology, 20(1), 1-6.
See Also
num.sv,sva_network
Examples
data(zma.se)
exp <- filter_by_variance(zma.se, n=500)
exp <- PC_correction(exp)
almeidasilvaf/BioNERO documentation built on Oct. 9, 2024, 1:49 a.m.
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View source: R/data_preprocess.R
| PC_correction | R Documentation |
Apply Principal Component (PC)-based correction for confounding artifacts
Description
Apply Principal Component (PC)-based correction for confounding artifacts
Usage
PC_correction(exp, verbose = FALSE)
Arguments
exp |
A gene expression data frame with genes in row names and samples in column names or a 'SummarizedExperiment' object. |
verbose |
Logical indicating whether to display progress messages or not. Default: FALSE. |
Value
Corrected expression data frame or 'SummarizedExperiment' object.
Author(s)
Fabricio Almeida-Silva
References
Parsana, P., Ruberman, C., Jaffe, A. E., Schatz, M. C., Battle, A., & Leek, J. T. (2019). Addressing confounding artifacts in reconstruction of gene co-expression networks. Genome biology, 20(1), 1-6.
See Also
num.sv,sva_network
Examples
data(zma.se)
exp <- filter_by_variance(zma.se, n=500)
exp <- PC_correction(exp)
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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