Thanks very much the code is working perfectly, but I hope guys that you can help me to do the same thing but by using the loop structure, i want to know if i am doing right, i want to use the loop structure to scan each sequence from the file sequence.txt (the file is attached) to get the frequency for each Amino Acid, and i wrote the following code so far, and i stopped, got confused, specially that i am a very beginner in R http://n4.nabble.com/file/n997581/sequence.txt sequence.txt : x<-read.table("sequence.txt",header=FALSE) AA<-c('A','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y')
test<-nchar(as.character(x$V1[i])) frequency<-function(X) { y<-rep(0,20) for(j in 1:test){ for(i in 1:nrow(x)){ res<-which(AA==substr(x$V1[i],j,j)) y[res]=y[res]+1 } } return(y) } So how to fix this code, how to give the life for the āiā and the ājā in order to initiate the indexing..... Sorry for bothering you guys. che wrote: > > may some one please help me to sort this out, i am trying to writ a R code > for calculating the frequencies of the amino acids in 9 different > sequences, i want the code to read the sequence from external text file, i > used the following code to do so: > x<-read.table("sequence.txt",header=FALSE) > > then i defined an array for 20 amino acids as following: > AA<-c('A','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y') > i am using the following code to calculate the frequencies: > > frequency<-function(X) > { > y<-rep(0,20) > for(j in 1:nchar(as.character(x$V1[i]))){ > for(i in 1:9){ > > res<-which(AA==substr(x$V1[i],j,j)) > y[res]=y[res]+1 > } > } > return(y) > } > > but this code actually is not working, it reads only one sequence, i dont > know why the loop is not working for the "i", which suppose to read the > nine rows of the file sequence.txt. the sequence.txt file is attached to > this message. > > cheers > http://n4.nabble.com/file/n997072/sequence.txt sequence.txt > -- View this message in context: http://n4.nabble.com/caculate-the-frequencies-of-the-Amino-Acids-tp997072p997581.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.