affiXcanGReX: Compute a GReX from variables and their coefficients for a...

In alussana/AffiXcan: A Functional Approach To Impute Genetically Regulated Expression

Description

Compute a GReX from variables and their coefficients for a set of genes

Usage

affiXcanGReX(affiXcanTraining, pcs, BPPARAM = bpparam())

Arguments

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")

Value

A SummarizedExperiment object containing the imputed GReX values

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)

testingTbaPaths <- system.file("extdata","testing.tba.toydata.rds",
package="AffiXcan")

pcs <- affiXcanPcs(tbaPaths=testingTbaPaths, affiXcanTraining=training,
scale=TRUE)

exprmatrix <- affiXcanGReX(affiXcanTraining=training, pcs=pcs)
}

alussana/AffiXcan documentation built on Oct. 20, 2020, 12:08 a.m.