find.DE.features: find.DE.features

In iDOS: Integrated Discovery of Oncogenic Signatures

find.DE.features

Description

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

Usage

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

Arguments

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

Value

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

Author(s)

Syed Haider

See Also

t.test, wilcox.test, var.test

Examples

# 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"
  );

iDOS documentation built on July 4, 2024, 1:09 a.m.