affiXcanPcs {AffiXcan} | R Documentation |
Compute PCs in MultiAssayExperiment objects using eigenvectors given by user
affiXcanPcs(tbaPaths, affiXcanTraining, scale, BPPARAM = bpparam())
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") |
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
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) }