R/getDS.R

In mjnueda/maSigPro: Significant Gene Expression Profile Differences in Time Course Gene Expression Data

getDS <- function(Model, vars="all", rsq=0.4)
{
  data<-Model$data
  gen<-Model$gen
  selected.genes <-Model$DSG
  Tfit2<-Model$Tfit

  data2 <- data[gen%in%selected.genes,]
  gen2 <- gen[gen%in%selected.genes]

#--------------------------------------------------------------------------------------
 get2 <- get.siggenes(Tfit2, vars=vars, rsq=rsq)
 sig.iso2 <- get2$summary
 gen.sig.iso2 <- as.character(gen2[rownames(data2)%in%sig.iso2])
 NumIso.by.gene <- tapply(sig.iso2, gen.sig.iso2, length) #Num of Transcripts from selected Isoforms
 DSG_distributed_by_number_of_DETs<-NumIso.by.gene
 T.iso2 <- table(DSG_distributed_by_number_of_DETs, useNA='ifany')

#--------------------------------------------------------------------------------------
print(paste(length(selected.genes)," DSG selected"))
print(paste(length(gen.sig.iso2)," DETs selected"))
print(T.iso2)

List0 <- setdiff(selected.genes, gen.sig.iso2) # list of DSG without any DET

out <- list(Model, get2, selected.genes, sig.iso2, List0, NumIso.by.gene)
names(out) <- c("Model", "get2", "DSG","DET","List0", "NumIso.by.gene")
out
}