PC_correction: Apply Principal Component (PC)-based correction for...

In almeidasilvaf/BioNERO: Biological Network Reconstruction Omnibus

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 March 25, 2024, 9:14 p.m.