Hey guys, I have what i think is a really simple problem :( I installed the seqinr library. I want to do an RSCU analysis. But i can't get it to work in even the simplest case. for example, if i have a string read in:> newdata5$testseq [1] "agtgagatgatagatagatagatagatagatagatagaccccccagata" and then i perform an RSCU analysis on it...> uco(newdata5,index="rscu")aaa aac aag aat aca acc acg act aga agc agg agt ata atc atg att caa cac cag cat NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA cca ccc ccg cct cga cgc cgg cgt cta ctc ctg ctt gaa gac gag gat gca gcc gcg gct NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA gga ggc ggg ggt gta gtc gtg gtt taa tac tag tat tca tcc tcg tct tga tgc tgg tgt NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA tta ttc ttg ttt NA NA NA NA it's telling me that there are no codons. I'm not sure how to split up the data or make this work at all. Any help appreciated. Aoife -- View this message in context: http://r.789695.n4.nabble.com/codon-usage-bias-tp4431740p4431740.html Sent from the R help mailing list archive at Nabble.com.
R. Michael Weylandt <michael.weylandt@gmail.com>
2012-Feb-29 16:37 UTC
[R] codon usage bias
This question sounds more suited for the Bioconductor list which focuses on R tools for genetic/bioinformatic computation. It's an active and very friendly list and I think one doesn't have to subscribe to post (but doing so certainly isn't a bad idea). Michael On Feb 29, 2012, at 9:55 AM, aoife <aoife.m.doherty at gmail.com> wrote:> Hey guys, I have what i think is a really simple problem :( > > I installed the seqinr library. I want to do an RSCU analysis. > > But i can't get it to work in even the simplest case. for example, if i have > a string read in: > >> newdata5 > $testseq > [1] "agtgagatgatagatagatagatagatagatagatagaccccccagata" > > > and then i perform an RSCU analysis on it... > > >> uco(newdata5,index="rscu") > aaa aac aag aat aca acc acg act aga agc agg agt ata atc atg att caa cac cag > cat > NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA > NA > cca ccc ccg cct cga cgc cgg cgt cta ctc ctg ctt gaa gac gag gat gca gcc gcg > gct > NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA > NA > gga ggc ggg ggt gta gtc gtg gtt taa tac tag tat tca tcc tcg tct tga tgc tgg > tgt > NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA > NA > tta ttc ttg ttt > NA NA NA NA > > > it's telling me that there are no codons. I'm not sure how to split up the > data or make this work at all. > Any help appreciated. > > Aoife > > > -- > View this message in context: http://r.789695.n4.nabble.com/codon-usage-bias-tp4431740p4431740.html > Sent from the R help mailing list archive at Nabble.com. > > ______________________________________________ > R-help at 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.