library(Rinbix) data(simrnaseq)
set.seed(1965) predictResult <- predictRnaseq(rnaseqCountsTrain=predictorsTrain, groupLabelsTrain=responseTrain, rnaseqCountsTest=predictorsTest, groupLabelsTest=responseTest, preprocessMethod="none", filterMethod="randomforests", topN=10, classifierMethod="svm", verbose=FALSE) predictResult
set.seed(1965) preprocessResult <- preprocessRnaseq(method="log2", predictorsTrain, predictorsTest, verbose=FALSE) cat("Before preprocessing:\n") predictorsTrain[1:5, 1:5] cat("After preprocessing:\n") preprocessResult$train[1:5, 1:5] filterResult <- filterRnaseq(method="randomforests", preprocessResult$train, responseTrain, preprocessResult$test, responseTest, nTopGenes=10, verbose=FALSE) cat("Genes before filtering:", ncol(preprocessResult$train), "after:", ncol(filterResult$train), "\n") classifyStats <- classifyRnaseq(method="svm", filterResult$train, responseTrain, filterResult$test, responseTest, verbose=FALSE) classifyStats
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