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

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

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, colname.score = "stemness_score")

Arguments

stemSig	is a vector of the stemness Signature generated using gelnet package. Please check the data from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5902191/ SC_PCBC_stemSig - Stemness Score DE_PCBC_stemSig - endoderm score EB_PCBC_stemSig - embryoid bodies score ECTO_PCBC_stemSig - ectoderm score MESO_PCBC_stemSig - mesoderm score
dataGE	is a matrix of Gene expression (genes in rows, samples in cols) from TCGAprepare
colname.score	Column name of the output. Default "stemness_score"

Value

table with samples and selected 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
 )
 Stemness_score <- TCGAanalyze_Stemness(
     stemSig = SC_PCBC_stemSig,
     dataGE = dataFilt,
     colname.score = "SC_PCBC_stem_score"
  )
 ECTO_score <- TCGAanalyze_Stemness(
     stemSig = ECTO_PCBC_stemSig,
     dataGE = dataFilt,
     colname.score = "ECTO_PCBC_stem_score"
  )
  MESO_score <- TCGAanalyze_Stemness(
     stemSig = MESO_PCBC_stemSig,
     dataGE = dataFilt,
     colname.score = "MESO_PCBC_stem_score"
  )

BioinformaticsFMRP/TCGAbiolinks documentation built on April 12, 2024, 2:08 a.m.