R/tableDS.R

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

tableDS <- function(seeDS)
{
  
  Model <- seeDS$Model
  get2 <- seeDS$get2
  cut <- seeDS$cut
  
  data <- Model$data
  gen <- Model$gen
  design<-Model$design
  
  sig.iso2 <- get2$summary
  gen.sig.iso2 <- as.character(gen[rownames(data)%in%sig.iso2])
  NT2<- seeDS$NumIso.by.gene

#------------------------------------------------------------
  data.clust <- get2$sig.genes$sig.profiles
  
 # Removing mono-DSG:
  
    genes.2 <- names(NT2[NT2>1])
    data.clust <- data.clust[gen.sig.iso2%in%genes.2,]
    gen.sig.iso22 <- gen.sig.iso2[gen.sig.iso2%in%genes.2]
    cut <- cut[sig.iso2[gen.sig.iso2%in%genes.2]]
 # renaming gen.sig.iso22 
    gen.sig.iso2<-gen.sig.iso22
  
#-------------------------------------------------------
# Identifying Major Isoform
#-------------------------------------------------------
  unic <- unique(gen.sig.iso2)
  G2 <- length(unic)
  Mayor=NULL
  for(j in 1:G2) 
  {
    zz<-data.clust[gen.sig.iso2==unic[j],]
    Mayor.j <- MayorIso(zz)
    names(Mayor.j)<-rownames(zz)
    Mayor<-c(Mayor, Mayor.j)
  }
  
cuts <-NULL
for(i in 1:length(unic))
{
  cutMi <- cut[gen.sig.iso2==unic[i] & Mayor==1]
  cutmi <- sort(unique(cut[gen.sig.iso2==unic[i] & Mayor==0]))
  if(length(cutmi)>1){
    cutmi<-f3(cutmi)
  }
  cuti<-c(cutMi,cutmi)
  cuts<-rbind(cuts,cuti)
  rownames(cuts)[i]<-unic[i]
}
cuts<-as.data.frame(cuts)
colnames(cuts)<-c("Cluster.Mayor", "Cluster.minor")
IsoTable <- table(cuts)

##----------------- RESULTS--------------------------------------------

out <- list(IsoTable, cuts )
names(out)<-c("IsoTable", "IsoClusters")
out
}


#---------------------------------------------------------------------------------------------------
# Auxiliar internal functions: f3, MayorIso  
#---------------------------------------------------------------------------------------------------

f3 <- function(x)
{
  x<-x[!is.na(x)]
  y<-x[1]
  for (i in 2:length(x))
  {
    y<-paste(y,x[i],sep="&")
  }
  y
}
# ejemplo:
# x<-c(1,2,4,NA,NA)
# f3(x)


#-------------------------------------------------------

MayorIso<-function(zz)
{
if( is.null(nrow(zz) )) 
{
 sol=1 }
else{
M <-apply(zz,1,sum)
sol=as.numeric(M==max(M))
}
sol
}