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.

makeCoefDf()

Make data.frame 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.