computePcs: Compute a matrix product between variables and eigenvectors
In AffiXcan: A Functional Approach To Impute Genetically Regulated Expression

Description Usage Arguments Value Examples

Compute a matrix product between variables and eigenvectors

1	computePcs(region, tbaMatrix, scale, pca)

`region`	A string, which is the name of the object in the list MultiAssayExperiment::experiments(tbaMatrix) that contains the TBA values of the genomic region of interest (see the param tbaMatrix)
`tbaMatrix`	A MultiAssayExperiment object containing the TBA values
`scale`	A logical; if scale=FALSE the TBA values will be only centered, not scaled before performing PCA
`pca`	The returningObject$pca from affiXcanTrain()

A data.frame containing the principal components values of the TBA in a certain genomic region, as the result of the matrix product between the TBA values and the eigenvectors

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)

region <- "ENSG00000256377.1"

tbaMatrixMAE <- readRDS(system.file("extdata","training.tba.toydata.rds",
package="AffiXcan"))

pca <- training$pca
pcs <- computePcs(region=region, tbaMatrix=tbaMatrixMAE, scale=TRUE, pca=pca)
}