Analysis code for all TCGA methylation data To use this code, firsly you may download the whole repository, then, one can type the following in shell:
Rscript EnMCB.R TCGA_CODE
which TCGA_CODE can be replaced by one of the TCGA Abbreviations as following:
LAML Acute Myeloid Leukemia
ACC Adrenocortical carcinoma
BLCA Bladder Urothelial Carcinoma
LGG Brain Lower Grade Glioma
BRCA Breast invasive carcinoma
CESC Cervical squamous cell carcinoma and endocervical adenocarcinoma
CHOL Cholangiocarcinoma
LCML Chronic Myelogenous Leukemia
COAD Colon adenocarcinoma
CNTL Controls
ESCA Esophageal carcinoma
FPPP FFPE Pilot Phase II
GBM Glioblastoma multiforme
HNSC Head and Neck squamous cell carcinoma
KICH Kidney Chromophobe
KIRC Kidney renal clear cell carcinoma
KIRP Kidney renal papillary cell carcinoma
LIHC Liver hepatocellular carcinoma
LUAD Lung adenocarcinoma
LUSC Lung squamous cell carcinoma
DLBC Lymphoid Neoplasm Diffuse Large B-cell Lymphoma
MESO Mesothelioma
MISC Miscellaneous
OV Ovarian serous cystadenocarcinoma
PAAD Pancreatic adenocarcinoma
PCPG Pheochromocytoma and Paraganglioma
PRAD Prostate adenocarcinoma
READ Rectum adenocarcinoma
SARC Sarcoma
SKCM Skin Cutaneous Melanoma
STAD Stomach adenocarcinoma
TGCT Testicular Germ Cell Tumors
THYM Thymoma
THCA Thyroid carcinoma
UCS Uterine Carcinosarcoma
UCEC Uterine Corpus Endometrial Carcinoma
UVM Uveal Melanoma
Before your analysis, please install R and our package EnMCB.
For your custom analysis, please modify the code in EnMCB.R.
All the TCGA clinical (survival) data are in the file "mmc1.xlsx".
If you encounter any kind of problem, please don't hesitate to contact me at [email protected] or [email protected]