selectedGenes: Accessors for the 'selectedGenes'.

In MLSeq: Machine Learning Interface for RNA-Seq Data

Description

This slot stores the name of selected genes which are used in the classifier. The trained model is stored in slot trainedModel. See trained for details.

Usage

selectedGenes(object)

## S4 method for signature 'MLSeq'
selectedGenes(object)

Arguments

object

an MLSeq object.

See Also

trained

Examples

## Not run: 
library(DESeq2)
data(cervical)

# a subset of cervical data with first 150 features.
data <- cervical[c(1:150), ]

# defining sample classes.
class <- data.frame(condition = factor(rep(c("N","T"), c(29, 29))))

n <- ncol(data)  # number of samples
p <- nrow(data)  # number of features

# number of samples for test set (30% test, 70% train).
nTest <- ceiling(n*0.3)
ind <- sample(n, nTest, FALSE)

# train set
data.train <- data[ ,-ind]
data.train <- as.matrix(data.train + 1)
classtr <- data.frame(condition = class[-ind, ])

# train set in S4 class
data.trainS4 <- DESeqDataSetFromMatrix(countData = data.train,
                   colData = classtr, formula(~ 1))

## Number of repeats (repeats) might change model accuracies ##
# Classification and Regression Tree (CART) Classification
cart <- classify(data = data.trainS4, method = "rpart",
          ref = "T", preProcessing = "deseq-vst",
          control = trainControl(method = "repeatedcv", number = 5,
                                 repeats = 3, classProbs = TRUE))

selectedGenes(cart)

## End(Not run)

MLSeq documentation built on Nov. 8, 2020, 5:37 p.m.