getDataTCGA {MoonlightR} | R Documentation |
This function retrieves and prepares TCGA data
getDataTCGA(cancerType, dataType, directory, cor.cut = 0.6, qnt.cut = 0.25, nSample, stage = "ALL", subtype = 0, samples = NULL)
cancerType |
select cancer type for which analysis should be run. panCancer for all available cancer types in TCGA. Defaults to panCancer |
dataType |
is dataType such as gene expression, cnv, methylation etc. |
directory |
Directory/Folder where the data was downloaded. Default: GDCdata |
cor.cut |
cor.cut |
qnt.cut |
qnt.cut |
nSample |
nSample |
stage |
stage |
subtype |
subtype |
samples |
samples |
returns filtered TCGA data
## Not run: dataFilt <- getDataTCGA(cancerType = "LUAD", dataType = "Gene expression", directory = "data", nSample = 4) ## End(Not run)