get_cancer_type: Get TCGA cancer type abbreviation

In wt12318/Easy_Bioinfo: Make some common bioinformatic workfolw easier to operate

Get TCGA cancer type abbreviation

Description

Return TCGA cancer type abbreviation for TCGA sample barcode, this function use the 6 and 7 position of sample barcode to extract cancer type based on the table of Tissue Source Site Codes of GDC, the description of this data can be seen at document by '?cancer_type_code'

Usage

get_cancer_type(
  input,
  cores,
  parallel = FALSE,
  need_full_name = FALSE,
  input_type = "code"
)

Arguments

input	TCGA tumor sample barcode or TCGA cancer type full name
cores	How many cores to use if parallelization is used, only can ce used when parallel is TRUE
parallel	Bool value, use parallelization or not, default FALSE
need_full_name	Bool value, return TCGA cancer type full name or not, default FALSE
input_type	"code" or "full_name" for input of TCGA tumor sample barcode or TCGA cancer type full name, respectively.

Value

cancer type

Examples

get_cancer_type("TCGA-OR-A5J1",par=FALSE)
get_cancer_type("Liver hepatocellular carcinoma",input_type="full_name")

wt12318/Easy_Bioinfo documentation built on June 17, 2022, 9:22 a.m.