R/IsoModel.R

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

IsoModel <- function(data, gen, design = NULL, Q = 0.05, min.obs = 6, minorFoldfilter = NULL, 
    counts = FALSE, family = NULL, theta = 10, epsilon = 1e-05) 
{
#---------------------------------------------------------------------------------------------------
# data is a matrix containing isoform expression. Isoforms must be in rows and experimental conditions in columns
# gen is a vector with the name of the gene each isoform belongs to
#---------------------------------------------------------------------------------------------------

Genes <- unique(gen)
g <- length(Genes)

 if (is.null(family)) {
        if (!counts) {
            family = gaussian()
        }
        if (counts) {
            family = negative.binomial(theta)
        }
    }

#---------------------------------------------------------------------------------------------------
# STEP -1: Remove cases with low expressed isoforms:
#---------------------------------------------------------------------------------------------------

print (paste(nrow(data), "transcripts"))
print (paste(length(unique(gen)), "genes"))

if (!is.null(minorFoldfilter)) {
  print ("Removing low expressed minor isoforms")
  moreOne <- names(which(table(gen) > 1))
  iso.sel <- NULL
  gene.sel <- NULL
  for ( i in moreOne) {
    which(gen==i)
    gene.data <- data[which(gen==i),]
    isoSUM <- apply(gene.data, 1, sum)
    major <- names(which(isoSUM == max(isoSUM)))[1]
    minors <- names(which(isoSUM != max(isoSUM)))
    div <- as.numeric(matrix(rep(gene.data[major,], length(minors)), ncol = ncol(data), length(minors), byrow = T)) / as.matrix(gene.data[minors,])
    is <- names(which(apply(div, 1, min, na.rm = T) < minorFoldfilter))
    iso.sel <- c(iso.sel, is)
    gene.sel <- c(gene.sel, rep(i, length(is)))
  }
  data <- data[iso.sel,]
  gen <- gene.sel
  print(dim(data))
  print(length(gen))
  print ("Done")
  print (paste(nrow(data), "remaining transcripts"))
  print (paste(length(unique(gen)), "remaining genes"))
}

#---------------------------------------------------------------------------------------------------
#  STEP 0: Remove cases with 1 transcript:
#---------------------------------------------------------------------------------------------------

 NT <- tapply(rownames(data),gen,length)
 Genes1 <- names(which(NT!=1))
 data1 <- data[gen%in%Genes1,]
 gen1 <- gen[gen%in%Genes1]
 Genes1 <- unique(gen1)
 g <- length(Genes1)
 dis <- as.data.frame(design$dis)
 mycolnames <- colnames(dis)

#---------------------------------------------------------------------------------------------------
# STEP 1: Gene models comparison. 
#---------------------------------------------------------------------------------------------------

pval<-NULL
 
 for(i in 1:g)
 {
 div <- c(1:round(g/100)) * 100
        if (is.element(i, div)) 
            print(paste(c("fitting gene", i, "out of", g), collapse = " "))

   zz <-data1[gen1==Genes1[i],]
   nt <- nrow(zz) 

 dis.gen <- REP(dis,nt)
 y <-  c(t(as.matrix(zz)))
 transcript<- factor(rep(c(1:nt),each = ncol(zz)))
 ydis <- cbind(y, dis.gen, transcript)
 
   model0 <- glm(Formula0(mycolnames), data=ydis,  family = family, epsilon = epsilon )
   model1 <- glm(Formula1(mycolnames), data=ydis,  family = family, epsilon = epsilon )

if(family$family=="gaussian")  {
    pvali <- anova(model0, model1, test="F")[2,6] }
else {
   pvali <- anova(model0,model1, test = "Chisq")[2,5] }
   names(pvali) <- Genes1[i]
   pval <- c(pval, pvali)
   }
 num.genes <- sum(p.adjust(pval)<Q, na.rm=TRUE)
 selected.genes <-names(sort(p.adjust(pval))[1:num.genes])

#---------------------------------------------------------------------------------------------------
# STEP 2: p.vector and T.fit to the transcripts that belong to selected.genes
#---------------------------------------------------------------------------------------------------
 data2 <- data[gen%in%selected.genes,]
 gen2 <- gen[gen%in%selected.genes]
 pvector2 <- p.vector(data2, design, counts=counts, item="isoform")
 Tfit2 <- T.fit(pvector2, item="isoform")

#---------------------------------------------------------------------------------------------------
# Output  
#---------------------------------------------------------------------------------------------------

ISO.SOL <-list(data, gen, design, selected.genes, pvector2, Tfit2)
names(ISO.SOL)<- c("data","gen", "design", "DSG","pvector","Tfit")
ISO.SOL
}


#---------------------------------------------------------------------------------------------------
# Auxiliar internal functions: REP, Formula0, Formula1  
#---------------------------------------------------------------------------------------------------

REP <- function(D,k)
{
r<-nrow(D)
c<-ncol(D)
DD<-NULL
for(i in 1:c)
{
DDi <- rep(D[,i],k)
DD <- cbind(DD,DDi)
}
colnames(DD)<-colnames(D)
as.data.frame(DD)
}

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

Formula0 <- function(names)
{
formula <- "y~"

if(length(names)==1){ formula=paste(formula,names[1],"+ transcript") }
else if(length(names)>1)
  {

  for (i in 1:(length(names)))
   {
   formula <- paste(formula,names[i],"+")
   }
formula <- paste(formula, "transcript")
}
formula <- as.formula(formula)
formula
}

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

Formula1 <- function(names)
{
formula <- "y~"

if(length(names)==1){ formula=paste(formula,names[1],"* transcript") }
else if(length(names)>1)
  {
formula <- paste(formula,"(" )
  for (i in 1:(length(names)-1))
   {
   formula <- paste(formula,names[i],"+")
   }
formula <- paste(formula,names[length(names)])
formula <- paste(formula, ") * transcript")
}
formula <- as.formula(formula)
formula
}