Accessors for the 'deseqTransform' slot of an MLSeq object

Description

Used transformation method for the trained model using classify function.

Usage

1
2
  ## S4 method for signature 'MLSeq'
deseqTransform(object)

Arguments

object

an MLSeq object

Details

deseqTransform slot stores the name of the transformation method either "vst" or "voomCPM"

Author(s)

Gokmen Zararsiz, Dincer Goksuluk, Selcuk Korkmaz, Vahap Eldem, Izzet Parug Duru, Turgay Unver, Ahmet Ozturk

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
data(cervical)

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

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

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

nTest = ceiling(n*0.2)  # number of samples for test set (20% test, 80% train).
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(~ condition))
data.trainS4 = DESeq(data.trainS4, fitType="local")

# Random Forest (RF) Classification
rf = classify(data = data.trainS4, method = "randomforest", normalize = "deseq", deseqTransform = "vst", cv = 5, rpt = 3, ref="T")

deseqTransform(rf)