TCGAanalyze_Stemness {TCGAbiolinks} | R Documentation

## Generate Stemness Score based on RNASeq (mRNAsi stemness index) Malta et al., Cell, 2018

### Description

TCGAanalyze_Stemness generate the mRNAsi score

### Usage

    TCGAanalyze_Stemness(stemSig, dataGE, annotation = FALSE)

### Arguments

`stemSig` | is a vector of the stemness Signature generated using gelnet package
`dataGE` | is a matrix of Gene expression (genes in rows, samples in cols) from TCGAprepare
`annotation` | as default is FALSE. If annotation == subtype it returns the molecular subtype of a sample. If annotation == sampleType it returns the type of a sample (normal or tumor)

### Value

table with samples and stemness score

### Examples

     # Selecting TCGA breast cancer (10 samples) for example stored in dataBRCA
     dataNorm <- TCGAanalyze_Normalization(tabDF = dataBRCA, geneInfo =  geneInfo)
     # quantile filter of genes
     dataFilt <- TCGAanalyze_Filtering(tabDF = dataNorm,
                                      method = "quantile",
                                      qnt.cut =  0.25)
     dataBRCA_stemness <- TCGAanalyze_Stemness(stemSig = PCBC_stemSig,
     dataGE = dataFilt, annotation = "sampleType")

[Package TCGAbiolinks version 2.12.6 Index]