affiXcanTrain {AffiXcan} | R Documentation

## Train the model needed to impute a GReX for each gene

### Description

Train the model needed to impute a GReX for each gene

### Usage

    affiXcanTrain(exprMatrix, assay, tbaPaths, regionAssoc, cov, varExplained,
      scale, BPPARAM = bpparam())

### Arguments

`exprMatrix` | A SummarizedExperiment object containing expression data
`assay` | A string with the name of the object in SummarizedExperiment::assays(exprMatrix) that contains expression values
`tbaPaths` | A vector of strings, which are the paths to MultiAssayExperiment RDS files containing the tba values
`regionAssoc` | A data.frame with the association between regulatory regions and expressed genes and with colnames = c("REGULATORY_REGION", "EXPRESSED_REGION")
`cov` | A data.frame with covariates values for the population structure where the columns are the PCs and the rows are the individual IIDs
`varExplained` | An integer between 0 and 100; varExplained=80 means that the principal components selected to fit the models must explain at least 80 percent of variation of TBA values
`scale` | A logical; if scale=FALSE the TBA values will be only centered, not scaled before performing PCA
`BPPARAM` | A BiocParallelParam object. Default is bpparam(). For details on BiocParallelParam virtual base class see browseVignettes("BiocParallel")

### Value

A list containing three objects: pca, bs, regionsCount

pca: A list containing lists named as the MultiAssayExperiment::experiments() found in the MultiAssayExperiment objects listed in the param tbaPaths. Each of these lists contains two objects:

eigenvectors: A matrix containing eigenvectors for those principal components selected according to the param varExplained

pcs: A matrix containing the principal components values selected according to the param varExplained

bs: A list containing lists named as the REGULATORY_REGIONS found in the param regionAssoc that have a correspondent colname in the experiments stored in MultiAssayExperiment objects listed in the param tbaPaths. Each of the lists in bs contains four objects:

coefficients: The coefficients of the principal components used in the model, completely similar to the "coefficients" 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

correctedP: The p value after the benjamini-hochberg correction for multiple testing, retrived using p.adjust(pvalues, method="BH")

regionsCount: An integer, that is the number of genomic regions taken into account during the training phase

### 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)
    }

[Package AffiXcan version 1.2.0 Index]