TCGAanalyze_Stemness: Generate Stemness Score based on RNASeq (mRNAsi stemness...

In TCGAbiolinks: TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

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")

TCGAbiolinks documentation built on Nov. 8, 2020, 5:37 p.m.