affiXcanPcs {AffiXcan}R Documentation

Compute PCs in MultiAssayExperiment objects using eigenvectors given by user

Description

Compute PCs in MultiAssayExperiment objects using eigenvectors given by user

Usage

affiXcanPcs(tbaPaths, affiXcanTraining, scale, BPPARAM = bpparam())

Arguments

tbaPaths

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

affiXcanTraining

The returning object from affiXcanTrain()

scale

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

BPPARAM

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

Value

A list of matrices containing the principal components values of TBA for each region; each object of the list is named after the MultiAssayExperiment object from which it derives

Examples

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

data(exprMatrix)
data(regionAssoc)
data(trainingCovariates)

assay <- "values"

training <- affiXcanTrain(exprMatrix=exprMatrix, assay=assay,
tbaPaths=trainingTbaPaths, regionAssoc=regionAssoc, cov=trainingCovariates,
varExplained=80, scale=TRUE)

testingTbaPaths <- system.file("extdata","testing.tba.toydata.rds",
package="AffiXcan")

regionsCount <- overlookRegions(testingTbaPaths)

pcs <- affiXcanPcs(tbaPaths=testingTbaPaths, affiXcanTraining=training,
scale=TRUE)
}

[Package AffiXcan version 1.0.0 Index]