[R] help, please! matrix operations inside 3 nested loops

[Fridolin]

hello, this is my script:

#1) read in data:
daten<-read.table('K:/Analysen/STRUCTURE/input_STRUCTURE_tab_excl_5_282_559.txt',
header=TRUE, sep="\t")
daten<-as.matrix(daten)

#2) create empty matrix:
indxind<-matrix(nrow=617, ncol=617) 
indxind[1:20,1:19]

#3) compare cells to each other, score:
for (s in 3:34) {   #walks though the matrix colum by colum, starting at
colum 3
  for (z1 in 1:617) {  #for each current colum, take one row (z1)...
    for (z2 in 1:617) {  #...and compare it to another row (z2) of the
current colum
      if (z1!=z2) {topf<-indxind[z1,z2]
                   if (daten[2*z1-1,s]==daten[2*z2-1,s]) topf<-topf+1  
#actually, 2 rows make up 1 individual,
                   if (daten[2*z1-1,s]==daten[2*z2,s]) topf<-topf+1     
#therefore i compare 2 rows
                   if (daten[2*z1,s]==daten[2*z2-1,s]) topf<-topf+1     
#with another 2 rows
                   if (daten[2*z1,s]==daten[2*z2,s]) topf<-topf+1
                   indxind[z1,z2]<-topf
                   indxind[z2,z1]<-topf
                  }
      #print(c(s,z1,z2,indxind[1,2])) ##counts s, z1 and z2 properly, but
gives NA for indxind[1,2]
      }
    #indxind[1:5,1:5] #empty matrix
  }
  #indxind[1:5,1:5] #empty matrix
  }

#4) check:
indxind[1:5,1:5]

this results no errors, but my matrix indxind remains empty (only NAs).
though all columns and rows are counted properly. R needs quite a while to
get through all this (there are probably smarter and faster ways to
calculate this but i am not too deep into R and bioinformatics, and i need
to calculate this only once). could the 3 for-loops already be too
computationally intense for adding matrix operations?

any help would be much appreciated!

thx, frido



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