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Apply Principal Component (PC)-based correction for confounding artifacts

Source: R/data_preprocess.R
PC_correction.Rd

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.

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

Author

Fabricio Almeida-Silva

Examples

data(zma.se)
exp <- filter_by_variance(zma.se, n=500)
exp <- PC_correction(exp)