moonlight {MoonlightR} | R Documentation

## moonlight pipeline

### Description

moonlight is a tool for identification of cancer driver genes. This function wraps the different steps of the complete analysis workflow. Providing different solutions:

1. MoonlighR::FEA

2. MoonlighR::URA

3. MoonlighR::PIA

### Usage

    moonlight(cancerType = "panCancer", dataType = "Gene expression",
      directory = "GDCdata", BPname = NULL, cor.cut = 0.6,
      qnt.cut = 0.25, Genelist = NULL, fdr.cut = 0.01, logFC.cut = 1,
      corThreshold = 0.6, kNearest = 3, nGenesPerm = 10,
      DiffGenes = FALSE, nBoot = 100, nTF = NULL, nSample = NULL,
      thres.role = 0, stage = NULL, subtype = 0, samples = NULL)

### Arguments

`cancerType` | select cancer type for which analysis should be run. panCancer for all available cancer types in TCGA. Defaults to panCancer
`dataType` | dataType
`directory` | directory
`BPname` | biological processes to use, if NULL: all processes will be used in analysis, RF for candidate; if not NULL the candidates for these processes will be determined (no learning)
`cor.cut` | cor.cut Threshold
`qnt.cut` | qnt.cut Threshold
`Genelist` | Genelist
`fdr.cut` | fdr.cut Threshold
`logFC.cut` | logFC.cut Threshold
`corThreshold` | corThreshold
`kNearest` | kNearest
`nGenesPerm` | nGenesPerm
`DiffGenes` | DiffGenes
`nBoot` | nBoot
`nTF` | nTF
`nSample` | nSample
`thres.role` | thres.role
`stage` | stage
`subtype` | subtype
`samples` | samples

### Value

table with cancer driver genes TSG and OCG.

### Examples

    dataDEGs <- DPA(dataFilt = dataFilt, dataType = "Gene expression")
    # to change with moonlight

[Package MoonlightR version 1.14.1 Index]