computeExpr: Compute the imputed GReX for a certain gene on a set of...
In AffiXcan: A Functional Approach To Impute Genetically Regulated Expression

Description Usage Arguments Value Examples

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

1	computeExpr(bs, pcs)

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()
p.val: The uncorrected anova pvalue of the model
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()

A vector of imputed GReX values

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)

region <- "ENSG00000256377.1"
bs <- training$bs[[region]]

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