computeRSquared: Compute R and R^2 between rows of two SummarizedExperiment...

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

Description

Compute R and R^2 between rows of two SummarizedExperiment assays

Usage

computeRSquared(
  realExpr,
  imputedExpr,
  assay,
  testingSamples = NULL,
  BPPARAM = bpparam()
)

Arguments

realExpr	A SummarizedExperiment object containing expression data
imputedExpr	The returning object of affiXcanImpute()
assay	A string with the name of the object in SummarizedExperiment::assays(realExpr) that contains expression values
testingSamples	A vector of strings. The identifiers of the samples that have to be considered by the function; default is NULL; if is.null(testingSamples)==TRUE then no filtering is performed
BPPARAM	A BiocParallelParam object. Default is bpparam(). For details on BiocParallelParam virtual base class see browseVignettes("BiocParallel")

Value

A list of lists; inner lists are named after the rows for which the correlation between realExpr and imputedExpr have been computed; inner lists contain two objects:

• rho: the pearson's correlation coefficient (R) between the real expression values and the imputed GReX for the cross-validation i on the expressed gene y, computed with cor()

• rho.sq: the coefficient of determination (R^2) between the real expression values and the imputed GReX for the cross-validation i on the expressed gene y, computed as pearson^2

• cor.test.p.val: the p-value of the cor.test() between the real expression values and the imputed GReX for the cross-validation i on the expressed gene y

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)

imputedExpr <- affiXcanImpute(tbaPaths=trainingTbaPaths,
affiXcanTraining=training, scale=TRUE)
realExpr <- exprMatrix

correlation <- computeRSquared(realExpr, imputedExpr, assay)
}

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