Function reference • metapredict

All functions

calcConfusionCv(): Calculate confusion matrix for cross-validation.

calcConfusionValidation(): Calculate confusion matrices (or matrix) for validation datasets.

downloadCustomCdfMappings(): Download custom CDF mapping files from Brainarray.

extractExpressionData(): Extract the expression matrices containing the desired samples.

getStudyData(): Get the gene expression data for one study.

getStudyDataList(): Get the gene expression data for multiple studies.

getSupportedPlatforms(): Get the GPLs for microarray platforms that are currently supported.

getUnsupportedPlatforms(): Get the GPLs for unsupported microarray platforms.

installCustomCdfPackages(): Install custom CDF packages from Brainarray.

makeCoefDt(): Make data.table of non-zero coefficients from a glmnet model.

makeGlmnetArgs(): Make arguments for glmnet.

mergeMatchStudyData(): Merge gene expression from different platforms that was measured on the same biological samples.

mergeStudyData(): Merge gene expression data from multiple studies.

metapredict(): Predict the response variable in validation datasets.

metapredictCv(): Perform cross-validation of merged gene expression data.

plotClassProbsCv(): Plot class probabilities for samples from cross-validation.

plotClassProbsValidation(): Plot class probabilities for samples from multiple validation datasets.

plotCoefficients(): Plot coefficients for a gene expression meta-analysis.

plotExpressionHeatmap(): Plot heatmap of merged gene expression data.