find.DE.features: find.DE.features
In iDOS: Integrated Discovery of Oncogenic Signatures

Description Usage Arguments Value Author(s) See Also Examples

Funtion to identify differentially expressed/variable features between Tumour (T) and Normal (N) profiles

find.DE.features(
  exp.data.T = NULL, 
  exp.data.N = NULL, 
  feature.ids = NULL,
  test.name = "t.test"
  )

`exp.data.T`	Feature by sample mRNA abundance matrix; tumour samples
`exp.data.N`	Feature by sample mRNA abundance matrix; normal/baseline samples
`feature.ids`	Vector of features to be used to estimate correlation
`test.name`	Specify the statistical test name (exactly as it appears in R). Supported tests are `t.test`, `wilcox.test`, `var.test`

Feature by cancer type matrix of log2 fold change (T vs N) and adjusted P values. P values are estimated through test.name

Syed Haider

t.test, wilcox.test, var.test

# load test data
x <- get.test.data(data.types = c("mRNA.T", "mRNA.N"));

# list of features to be assessed for differential expression
feature.ids <- rownames(x$mRNA.T$BLCA);

DE.results <- find.DE.features(
  exp.data.T = x$mRNA.T, 
  exp.data.N = x$mRNA.N, 
  feature.ids = feature.ids,
  test.name = "t.test"
  );