## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(dpi = 300) knitr::opts_chunk$set(cache = FALSE) ## ----echo = FALSE,hide=TRUE, message=FALSE,warning=FALSE---------------------- library(TCGAbiolinks) ## ----message=FALSE, warning=FALSE, include=FALSE------------------------------ library(SummarizedExperiment) library(dplyr) library(DT) ## ----eval = TRUE, message = FALSE, results = "hide"--------------------------- # 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 ) data(SC_PCBC_stemSig) Stemness_score <- TCGAanalyze_Stemness( stemSig = SC_PCBC_stemSig, dataGE = dataFilt ) data(ECTO_PCBC_stemSig) ECTO_score <- TCGAanalyze_Stemness( stemSig = ECTO_PCBC_stemSig, dataGE = dataFilt, colname.score = "ECTO_PCBC_stem_score" ) data(MESO_PCBC_stemSig) MESO_score <- TCGAanalyze_Stemness( stemSig = MESO_PCBC_stemSig, dataGE = dataFilt, colname.score = "MESO_PCBC_stem_score" ) ## ----eval = T----------------------------------------------------------------- head(Stemness_score) head(ECTO_score) head(MESO_score)