Sara Kamali
2011-Aug-16 20:15 UTC
[R] count dinucleotides in DNA using "count " function in "seqinr" package
Dear all
I want to count the number of dinucleotides of multiple DNA sequences from a csv
file seprately using "count" function in "seqinr" package .
it works for one sequence , but when I put this function in a for loop it gives
zero for all nucleotides .
i would be thankful if someone can help me.
here is my code:
#there are 4 DNA sequences in my CSV file.
seq<-read.csv("F:/input.csv",head=TRUE,sep=",")
row<-nrow(seq)
col<-ncol(seq)
for(i in 1:row)
{
#p<-s2c(seq[i])
x=count(seq[1]$head[i], 2 , alphabet = s2c("acgt"))
print(x)
}
and here is the output :
aa ac ag at ca cc cg ct ga gc gg gt ta tc tg tt
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
aa ac ag at ca cc cg ct ga gc gg gt ta tc tg tt
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
aa ac ag at ca cc cg ct ga gc gg gt ta tc tg tt
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
aa ac ag at ca cc cg ct ga gc gg gt ta tc tg tt
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
awaiting for your help
Regards
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