Nothing
"pseudo_counts" <-
function(profile1){
## This will calculate the pseudocounts based on
## f(a,i) = n(a,i) + E*(Sumj n(j,i)*Matrix(j,a))
## -------------------------------------
## n(i) + E
## Where E is the number of pseudocounts to add
## This is the Heinikoff method
## profile1 is generated by create_profile()
## Create the probability matrix
probab<-create_probab()
len<-dim(profile1)[2]
## Sequence Count, assuming at least one ungapped column.
sequence_count<-max(apply(profile1,2,sum))
profile_result<-profile1
for(k in 1:len){
for(j in 1:20){
sum_col<-0
sequence_count<-sum(profile1[,k])
## Bc=m*Rc where Rc is the number of different residues
counts <- 5*sum(profile1[,k]>0)
if(sequence_count > 0){
total<-0
for(i in 1:20){
sum_col<-sum_col+(profile1[i,k]/sequence_count)*(probab[i,j]/(sum(probab[,i])))
total<-total+(probab[i,j]/(sum(probab[,i])))
}
}
profile_result[j,k] <- (profile1[j,k]+(counts*sum_col))/(sequence_count+counts)
}
}
## Return the number of extra counts for each amino acid,
return(profile_result)
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.