Parameters obtained via FireBrowse
See also
Other functions associated with TCGA data retrieval:
getDownloadsFolder(),
isFirebrowseUp(),
loadTCGAdata(),
parseTCGAsampleTypes()
Examples
getTCGAdataTypes()
#> $`RNA sequencing`
#> Junction quantification Exon quantification Exon expression
#> "junction_quantification" "exon_quantification" "exon_expression"
#> Junction expression RSEM genes RSEM genes normalized
#> "junction_expression" "RSEM_genes" "RSEM_genes_normalized"
#> RSEM isoforms Preprocess
#> "RSEM_isoforms" "Preprocess"
#>
if (isFirebrowseUp()) getTCGAdates()
#> [1] "2016-01-28" "2015-11-01" "2015-08-21" "2015-06-01" "2015-04-02"
#> [6] "2015-02-04" "2014-12-06" "2014-10-17" "2014-09-02" "2014-07-15"
#> [11] "2014-05-18" "2014-04-16" "2014-03-16"
if (isFirebrowseUp()) getTCGAcohorts()
#> ACC
#> "Adrenocortical carcinoma"
#> BLCA
#> "Bladder Urothelial Carcinoma"
#> BRCA
#> "Breast invasive carcinoma"
#> CESC
#> "Cervical squamous cell carcinoma and endocervical adenocarcinoma"
#> CHOL
#> "Cholangiocarcinoma"
#> COAD
#> "Colon adenocarcinoma"
#> COADREAD
#> "Colorectal adenocarcinoma"
#> DLBC
#> "Lymphoid Neoplasm Diffuse Large B-cell Lymphoma"
#> ESCA
#> "Esophageal carcinoma "
#> FPPP
#> "FFPE Pilot Phase II"
#> GBM
#> "Glioblastoma multiforme"
#> GBMLGG
#> "Glioma"
#> HNSC
#> "Head and Neck squamous cell carcinoma"
#> KICH
#> "Kidney Chromophobe"
#> KIPAN
#> "Pan-kidney cohort (KICH+KIRC+KIRP)"
#> KIRC
#> "Kidney renal clear cell carcinoma"
#> KIRP
#> "Kidney renal papillary cell carcinoma"
#> LAML
#> "Acute Myeloid Leukemia"
#> LGG
#> "Brain Lower Grade Glioma"
#> LIHC
#> "Liver hepatocellular carcinoma"
#> LUAD
#> "Lung adenocarcinoma"
#> LUSC
#> "Lung squamous cell carcinoma"
#> MESO
#> "Mesothelioma"
#> 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"
#> STES
#> "Stomach and Esophageal carcinoma"
#> TGCT
#> "Testicular Germ Cell Tumors"
#> THCA
#> "Thyroid carcinoma"
#> THYM
#> "Thymoma"
#> UCEC
#> "Uterine Corpus Endometrial Carcinoma"
#> UCS
#> "Uterine Carcinosarcoma"
#> UVM
#> "Uveal Melanoma"