iDOS (version 1.0.1)

find.DE.features: 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"
  )

Value

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

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

Author

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"
  );