computePcs {AffiXcan} | R Documentation |
Compute a matrix product between variables and eigenvectors
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) }