affiXcanImpute {AffiXcan} | R Documentation

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

### 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)

[Package AffiXcan version 1.8.0 Index]