Hi fadialnaji, Take a look at the Biostring package in Bioconductor [1] It might be an alternative to do what you want.
HTH, Jorge [1] http://www.bioconductor.org/packages/release/bioc/html/Biostrings.html On Fri, Jan 1, 2010 at 11:59 PM, 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-tp997072p997072.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. > [[alternative HTML version deleted]] ______________________________________________ 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.
