Nothing
setGeneric("KolmogorovSmirnovSelection", function(measurements, ...)
{standardGeneric("KolmogorovSmirnovSelection")})
# Matrix of numeric measurements.
setMethod("KolmogorovSmirnovSelection", "matrix", function(measurements, classes, ...)
{
KolmogorovSmirnovSelection(DataFrame(t(measurements), check.names = FALSE), classes, ...)
})
setMethod("KolmogorovSmirnovSelection", "DataFrame", # Clinical data or one of the other inputs, transformed.
function(measurements, classes, datasetName,
trainParams, predictParams, resubstituteParams, ...,
selectionName = "Kolmogorov-Smirnov Test", verbose = 3)
{
splitDataset <- .splitDataAndClasses(measurements, classes)
measurements <- splitDataset[["measurements"]]
isNumeric <- sapply(measurements, is.numeric)
measurements <- measurements[, isNumeric, drop = FALSE]
if(sum(isNumeric) == 0)
stop("No features are numeric but at least one must be.")
if(verbose == 3)
message("Selecting features by Kolmogorov Smirnov distance.")
oneClass <- classes == levels(classes)[1]
otherClass <- classes == levels(classes)[2]
KSdistance <- apply(measurements, 2, function(featureColumn)
stats::ks.test(featureColumn[oneClass], featureColumn[otherClass], ...)[["statistic"]])
orderedFeatures <- order(KSdistance, decreasing = TRUE)
.pickFeatures(measurements, classes, NULL, datasetName,
trainParams, predictParams, resubstituteParams,
orderedFeatures, selectionName, verbose)
})
# One or more omics data sets, possibly with clinical data.
setMethod("KolmogorovSmirnovSelection", "MultiAssayExperiment",
function(measurements, targets = names(measurements), ...)
{
tablesAndClasses <- .MAEtoWideTable(measurements, targets)
dataTable <- tablesAndClasses[["dataTable"]]
classes <- tablesAndClasses[["classes"]]
if(ncol(dataTable) == 0)
stop("No variables in data tables specified by \'targets\' are numeric.")
else
KolmogorovSmirnovSelection(dataTable, classes, ...)
})
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