cgMutation: convenient shortcut to find mutations

In ilwookkim/TCGANetwork: Gene co-expression network

Description

convenient shortcut to find mutations

Usage

cgMutation(
  cgds,
  cancer_study_id,
  genes = NA,
  caselist_name = "Samples with mutation data"
)

Arguments

cgds	object, output from the cgBase() function
cancer_study_id	string, the as given in the cgBase() printout
genes	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.
caselist_name	string, should be chosen so that only samples with mutation data are used.

Value

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

Examples

cgds <- cgBbase()
mystudy <- "laml_tcga"
myMutations <- cgData(cgds, mystudy, genes=c("FLT3","TP53"))

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