getDataTCGA {MoonlightR} | R Documentation

## getDataTCGA

### Description

This function retrieves and prepares TCGA data

### Usage

    getDataTCGA(cancerType, dataType, directory, cor.cut = 0.6, qnt.cut = 0.25,
      nSample, stage = "ALL", subtype = 0, samples = NULL, seed = 12345)

### Arguments

`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
`seed` | set to get same result

### Value

returns filtered TCGA data

### Examples

    ## Not run:
    dataFilt <- getDataTCGA(cancerType = "LUAD",
    dataType = "Gene expression", directory = "data", nSample = 4)

    ## End(Not run)

[Package MoonlightR version 1.6.1 Index]