computeExpr {AffiXcan}R Documentation

Compute the imputed GReX for a certain gene on a set of individuals

Description

Compute the imputed GReX for a certain gene on a set of individuals

Usage

computeExpr(bs, pcs)

Arguments

bs

A list containing three objects:

coefficients: An object containing the coefficients of the principal components used in the model, completely similar to the "coefficients" object from the results of lm()

pval: The uncorrected anova pvalue of the model, retrieved from anova(model, modelReduced, test="F")$'Pr(>F)'[2]

r.sq: The coefficient of determination between the real total expression values and the imputed GReX, retrived from summary(model)$r.squared

pcs

A list, which is the returning object of affiXcanPcs()

Value

A summarizedExperiment object; SummarizedExperiment::assays(returningObject)$GReX is a matrix 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)

bs <- training$bs

exprmatrix <- computeExpr(bs=bs, pcs=pcs)
}

[Package AffiXcan version 1.2.0 Index]