R/CreateGeneFuPreds.R

In abc-igmm/transcripTools: Collection of functions for analysing gene expression data

CreateGenefuPreds <- function(expressionDF_entrez){
  
  an.dfr_entrez <- CreateAnnotationDataframe_entrez(expressionDF = expressionDF_entrez)
  
  exp.hgnc <- idReplace(expressionDF_entrez, format_in = "entrezgene", "hgnc_symbol")
  an.dfr_hgnc <- CreateAnnotationDataframe_hgnc(exp.hgnc)
  
  
  mammaprint_risk <- gene70(data = t(expressionDF_entrez), annot = an.dfr_entrez, do.mapping = TRUE)$risk %>% as.data.frame()
  rorS_risk <- rorS(data = t(expressionDF_entrez), annot = an.dfr_entrez, do.mapping = TRUE)$risk %>% as.data.frame()
  
  mammaprint_score <- gene70(data = t(expressionDF_entrez), annot = an.dfr_entrez, do.mapping = TRUE)$score %>% as.data.frame()
  rorS_score <- rorS(data = t(expressionDF_entrez), annot = an.dfr_entrez, do.mapping = TRUE)$score %>% as.data.frame()
  
  scmgene <- molecular.subtyping(
    sbt.model = c("scmgene"), 
    data = t(expressionDF_entrez), 
    annot = an.dfr_entrez, do.mapping = TRUE)$subtype %>% 
    as.data.frame()
  
  scmod1 <- molecular.subtyping(
    sbt.model = c("scmod1"), 
    data = t(expressionDF_entrez), 
    annot = an.dfr_entrez, do.mapping = TRUE)$subtype %>% 
    as.data.frame()
  
  scmod2 <- molecular.subtyping(
    sbt.model = c("scmod2"), 
    data = t(expressionDF_entrez), 
    annot = an.dfr_entrez, do.mapping = TRUE)$subtype %>% 
    as.data.frame()
  
  pam50 <- molecular.subtyping(
    sbt.model = c("pam50"), 
    data = t(expressionDF_entrez), 
    annot = an.dfr_entrez, do.mapping = TRUE)$subtype %>% 
    as.data.frame()
  
  ssp2006 <- molecular.subtyping(
    sbt.model = c("ssp2006"), 
    data = t(expressionDF_entrez), 
    annot = an.dfr_entrez, do.mapping = TRUE)$subtype %>% 
    as.data.frame()
  
  ssp_2003 <- molecular.subtyping(
    sbt.model = c("ssp2003"), 
    data = t(expressionDF_entrez), 
    annot = an.dfr_entrez, do.mapping = TRUE)$subtype %>% 
    as.data.frame()
  
  intClust <- molecular.subtyping(
    sbt.model = c("intClust"), 
    data = t(exp.hgnc), 
    annot = an.dfr_hgnc, do.mapping = TRUE)$subtype %>% 
    as.data.frame()
  
  AIMS <- molecular.subtyping(
    sbt.model = c("AIMS"), 
    data = t(expressionDF_entrez), 
    annot = an.dfr_entrez, do.mapping = TRUE)$subtype %>% 
    as.data.frame()
  
  subtypes <- cbind(scmgene, scmod1, scmod2, pam50, ssp2006, ssp_2003, intClust, AIMS, mammaprint_risk, mammaprint_score, rorS_risk, rorS_score)
  colnames(subtypes) <- c("scmgene", "smcod1", "scmod2", "pam50", "ssp2006", "ssp2003", "IC10", "AIMS", "MammaPrint_risk", "MammaPrint_score", "rorS_risk", "rorS_score")
  subtypes
}