affiXcanImpute: Impute a GReX for each gene for which a model was generated

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

Description

Impute a GReX for each gene for which a model was generated

Usage

affiXcanImpute(tbaPaths, affiXcanTraining, scale = TRUE, BPPARAM = bpparam())

Arguments

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; default is TRUE
BPPARAM	A BiocParallelParam object. Default is bpparam(). For details on BiocParallelParam virtual base class see browseVignettes("BiocParallel")

Value

A SummarizedExperiment object containing imputed GReX values

Examples

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,
varExplained=80, scale=TRUE)

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

exprmatrix <- affiXcanImpute(tbaPaths=testingTbaPaths,
affiXcanTraining=training, scale=TRUE)

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