computePcs {AffiXcan} | R Documentation

## Compute a matrix product between variables and eigenvectors

### Description

Compute a matrix product between variables and eigenvectors

### Usage

    computePcs(region, tbaMatrix, scale, pca)

### Arguments

`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()

### Value

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

### 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)

    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)
    }

[Package AffiXcan version 1.4.0 Index]