Learn R Programming

miRLAB (version 1.2.2)

getData: Get data from TCGA

Description

Download matched miRNA and mRNA expression profiles from TCGA using TCGA Assembler. In order to this function to work, users need to download the the file "DirectoryTraverseResult_Jul-08-2014.rda" from nugget.unisa.edu.au/Thuc/miRLAB/ and place it in the working directory

Usage

getData(CancerName)

Arguments

CancerName
The name of cancer using abbreviation of cancer name as one of the followings:
  • Adrenocortical carcinoma: ACC
  • Bladder urothelial carcinoma: BLCA
  • Breast invasive carcinoma: BRCA
  • Cervical squamous cell carcinoma and endocervical adenocarcinoma: CESC
  • Colon adenocarcinoma: COAD
  • Lymphoid neoplasm diffuse large B-cell lymphoma: DLBC
  • Esophageal carcinoma: ESCA
  • Glioblastoma multiforme: GBM
  • Head and neck squamous cell carcinoma: HNSC
  • Kidney chromophobe: KICH
  • Kidney renal clear cell carcinoma: KIRC
  • Kidney renal papillary cell carcinoma: KIRP
  • Acute myeloid leukemia: LAML
  • Brain lower grade glioma: LGG
  • Liver hepatocellular carcinoma: LIHC
  • Lung adenocarcinoma: LUAD
  • Lung squamous cell carcinoma: LUSC
  • Ovarian serous cystadenocarcinoma: OV
  • Pancreatic adenocarcinoma: PAAD
  • Prostate adenocarcinoma: PRAD
  • Rectum adenocarcinoma: READ
  • Sarcoma: SARC
  • Skin cutaneous melanoma: SKCM
  • Stomach adenocarcinoma: STAD
  • Thyroid carcinoma: THCA
  • Uterine corpus endometrial carcinoma: UCEC
  • Uterine carcinosarcoma: UCS

Value

  • Dataset of matched miRNA and mRNA expression profiles

References

Zhu, Y., Qiu, P., and Ji, Y. (2014). TCGA-Assembler: open-source software for retrieving and processing TCGA data. Nat. Methods, 11, 599-600.

Examples

Run this code
BreastCancer=getData("BRCA")

Run the code above in your browser using DataLab