## ------------------------------------------------------------------------
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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