PC_correction {BioNERO} | 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)

[Package BioNERO version 1.0.4 Index]