affiXcanGReX {AffiXcan} | R Documentation |
Compute a GReX from variables and their coefficients for a set of genes
affiXcanGReX(affiXcanTraining, pcs, BPPARAM = bpparam())
affiXcanTraining |
The returning object from affiXcanTrain() |
pcs |
A list, which is the returning object from affiXcanPcs() |
BPPARAM |
A BiocParallelParam object. Default is bpparam(). For details on BiocParallelParam virtual base class see browseVignettes("BiocParallel") |
A SummarizedExperiment object containing the imputed GReX values
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") pcs <- affiXcanPcs(tbaPaths=testingTbaPaths, affiXcanTraining=training, scale=TRUE) bs <- training$bs exprmatrix <- affiXcanGReX(affiXcanTraining=training, pcs=pcs) }