## ----------------------------------------------------------------------------- suppressMessages(library(MultiAssayExperiment)) tba <- readRDS(system.file("extdata","training.tba.toydata.rds", package="AffiXcan")) ## This is a MultiAssayExperiment object names(assays(tba)) ## ----------------------------------------------------------------------------- assays(tba)$ENSG00000139269.2[1:5,1:4] ## ----------------------------------------------------------------------------- suppressMessages(library(SummarizedExperiment)) load("../data/exprMatrix.RData") assays(exprMatrix)$values[,1:5] ## ----------------------------------------------------------------------------- load("../data/regionAssoc.RData") regionAssoc[1:3,] ## ----------------------------------------------------------------------------- load("../data/trainingCovariates.RData") head(trainingCovariates) ## ----------------------------------------------------------------------------- suppressMessages(library("AffiXcan")) 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") exprmatrix <- affiXcanImpute(tbaPaths=testingTbaPaths, affiXcanTraining=training, scale=TRUE) grexMatrix <- assays(exprmatrix)$GReX as.data.frame(grexMatrix)[,1:5] ## ----------------------------------------------------------------------------- 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, kfold=5)