Description Usage Arguments Value Examples

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

1 2 3 4 5 6 7 | ```
computeRSquared(
realExpr,
imputedExpr,
assay,
testingSamples = NULL,
BPPARAM = bpparam()
)
``` |

`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") |

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

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | ```
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)
}
``` |

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