affiXcanPca {AffiXcan}R Documentation

Perform a PCA on each experiment found in MultiAssayExperiment objects

Description

Perform a PCA on each experiment found in MultiAssayExperiment objects

Usage

affiXcanPca(tbaPaths, varExplained, scale, regionsCount,
  BPPARAM = bpparam())

Arguments

tbaPaths

A vector of strings, which are the paths to MultiAssayExperiment RDS files containing the tba values

varExplained

An integer between 0 and 100; varExplained=80 means that the principal components selected to fit the models must explain at least 80 percent of variation of TBA values

scale

A logical; if scale=FALSE the TBA values will be only centered, not scaled before performing PCA

regionsCount

An integer, that is the summation of length(assays()) of every MultiAssayExperiment RDS object indicated in the param tbaPaths; it is the returning value from overlookRegions()

BPPARAM

A BiocParallelParam object. Default is bpparam(). For details on BiocParallelParam virtual base class see browseVignettes("BiocParallel")

Value

pca: A list containing lists named as the MultiAssayExperiment::experiments() found in the MultiAssayExperiment objects listed in the param tbaPaths. Each of these lists contains two objects:

eigenvectors: A matrix containing eigenvectors for those principal components selected according to the param varExplained

pcs: A matrix containing the principal components values selected according to the param varExplained

Examples

if (interactive()) {
tbaPaths <- system.file("extdata","training.tba.toydata.rds",
package="AffiXcan")
regionsCount <- overlookRegions(tbaPaths)

pca <- affiXcanPca(tbaPaths=tbaPaths, varExplained=80, scale=TRUE,
regionsCount=regionsCount)
}

[Package AffiXcan version 1.2.0 Index]