estimate.expression.cna.correlation: estimate.expression.cna.correlation

In iDOS: Integrated Discovery of Oncogenic Signatures

Description

Estimate subtype specific correlation between mRNA and CNA profiles

Usage

estimate.expression.cna.correlation(
  exp.data = NULL, 
  cna.data.log2 = NULL, 
  corr.threshold = 0.3, 
  corr.direction = "two.sided", 
  subtypes.metadata = NULL, 
  feature.ids = NULL, 
  cancer.type = NULL, 
  data.dir = NULL, 
  graphs.dir = NULL
  )

Arguments

exp.data	Feature by sample mRNA abundance matrix
cna.data.log2	Feature by sample CNA log ratio matrix
corr.threshold	Threshold for Spearman's Rho to consider a feature as candidate driver
corr.direction	Whether to include positively (greater), negatively (less) or both (two.sided) correlated features. Defaults to two.sided
subtypes.metadata	Subtypes metadata list of lists. Must contain at least one subtype specific samples using list subtype.samples.list. If no subtypes are present, specify list element "All" with all samples
feature.ids	Vector of features to be used to estimate correlation
cancer.type	Name of the cancer type or dataset
data.dir	Path to output directory where mRNA and CNA correlation statistics will be stored
graphs.dir	Path to graphs directory

Value

A list of lists containing correlated features per cancer subtype

Author(s)

Syed Haider

Examples

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

# temporary output directory
tmp.output.dir <- tempdir();

# estimate mRNA and CNA correlation
correlated.features <- estimate.expression.cna.correlation(
  exp.data = x$mRNA.T$BLCA, 
  cna.data.log2 = x$CNA.log2$BLCA, 
  corr.threshold = 0.3, 
  corr.direction = "two.sided", 
  subtypes.metadata = list(
    "subtype.samples.list" = list("All" = colnames(x$mRNA.T$BLCA))
    ), 
  feature.ids = rownames(x$mRNA.T$BLCA), 
  cancer.type = "BLCA", 
  data.dir = paste(tmp.output.dir, "/data/BLCA/", sep = ""),
  graphs.dir = paste(tmp.output.dir, "/graphs/BLCA/", sep = "")
  );

iDOS documentation built on May 2, 2019, 2:28 p.m.