TCGAanalyze_Stemness {TCGAbiolinks} | R Documentation |
TCGAanalyze_Stemness generate the mRNAsi score
TCGAanalyze_Stemness(stemSig, dataGE, annotation = FALSE)
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) |
table with samples and stemness score
# 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")