cgData: output data of the specified type

In ilwookkim/TCGANetwork: Gene co-expression network

Description

output data of the specified type

Usage

cgData(
  cgds,
  cancer_study_id,
  profile_name,
  caselist_name = "All samples",
  genes = NA,
  dropNApatients = T
)

Arguments

cgds	object, output from the cgBase() function
cancer_study_id	string, the ID as given in the first column of the cgBase() printout
profile_name	string, profile name (not ID) to be used (obtained from the printout of the cgStudy() function)
caselist_name	string, caselist name (not ID) to be used (obtained from the printout of the cgStudy() function)
genes	string vector with genes of interest. Symbols, EntrezIds and EnsemblIds work. If nothing (NA) is provided, all genes in the GO database will be used. This will take some time, so if you only need a specific set of genes, specify it here.
dropNApatients	boolean, should patients with only NA values be dropped? For mutation data, turn this to FALSE, otherwise non-mutated patients will drop out.

Value

data.frame, each row is a patient, each column is a gene

Examples

cgds <- cgBbase()
mystudy <- "laml_tcga"
cgStudy(cgds, mystudy)
myData <- cgData(cgds, mystudy, "mRNA expression (RNA Seq RPKM)", "TP53")

ilwookkim/TCGANetwork documentation built on March 31, 2021, 4:03 p.m.