TCGA data obtained via FireBrowse
Usage
loadTCGAdata(
folder = getDownloadsFolder(),
data = c("clinical", "junction_quantification", "RSEM_genes"),
exclude = c(".aux.", ".mage-tab.", "MANIFEST.txt"),
...,
download = TRUE
)Arguments
- folder
Character: directory to store the downloaded archives (by default, saves to
getDownloadsFolder())- data
Character: data to load (see
getTCGAdataTypes())- exclude
Character: files and folders to exclude from downloading and from loading into R (by default, exclude files containing
.aux.,.mage-tab.andMANIFEST.TXT)- ...
Arguments passed on to
queryFirebrowseDatadateCharacter: dates of the data retrieval by FireBrowse (by default, it uses the most recent data available)
cohortCharacter: abbreviation of the cohorts (by default, returns data for all cohorts)
data_typeCharacter: data types (optional)
toolCharacter: data produced by the selected FireBrowse tools (optional)
platformCharacter: data generation platforms (optional)
centerCharacter: data generation centres (optional)
levelInteger: data levels (optional)
protocolCharacter: sample characterization protocols (optional)
pageInteger: page of the results to return (optional)
page_sizeInteger: number of records per page of results (optional)
sort_byString: column used to sort the data (by default, sort by cohort)
- download
Boolean: download missing files
Value
A list with the loaded data, unless required files are unavailable
and download = FALSE (if so, it returns the URL of files to download)
See also
Other functions associated with TCGA data retrieval:
getDownloadsFolder(),
getTCGAdataTypes(),
isFirebrowseUp(),
parseTCGAsampleTypes()
Other functions to load data:
loadGtexData(),
loadLocalFiles(),
loadSRAproject()
Examples
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"
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 (FALSE) { # \dontrun{
loadTCGAdata(cohort = "ACC", data_type = "Clinical")
} # }