Good afternoon. I am a master student in University of Porto in Portugal. At this moment I’m starting to use R, so I have some doubts. The aim of my analysis is: calculate a pairwise FST matrix from fasta file and creat a principal component analyses with adegenet package (I use seqinr and ape package to read this file, then I convert this file into a genind object with DNA2genind function provide in adegenet package). After convert my file the pairwise.fst function is not found. If you could help me would be great. Greetings: Rui Oliveira -- ------------------------------------------------------------------- Rui Manuel Oliveira [[alternative HTML version deleted]]
Homework? We try not to do homework on this list. -- Bert On Thu, Jul 28, 2011 at 8:11 AM, Rui Oliveira <rui18oliver at gmail.com> wrote:> Good afternoon. > > I am a master student in University of Porto in Portugal. At this moment I?m > starting to use R, so I have some doubts. > > The aim of my analysis is: ?calculate a pairwise FST matrix from fasta file > and creat a principal component analyses with adegenet package (I use seqinr > and ape package to read this file, then I convert this file into a genind > object with DNA2genind function provide in adegenet package). After convert > my file the pairwise.fst function is not found. > > If you could help me would be great. > > Greetings: Rui Oliveira > > -- > ------------------------------------------------------------------- > Rui Manuel Oliveira > > ? ? ? ?[[alternative HTML version deleted]] > > > ______________________________________________ > 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. > >-- "Men by nature long to get on to the ultimate truths, and will often be impatient with elementary studies or fight shy of them. If it were possible to reach the ultimate truths without the elementary studies usually prefixed to them, these would not be preparatory studies but superfluous diversions." -- Maimonides (1135-1204) Bert Gunter Genentech Nonclinical Biostatistics
On Jul 28, 2011, at 11:35 AM, Bert Gunter wrote:> Homework? > > We try not to do homework on this list.> > -- Bert > > On Thu, Jul 28, 2011 at 8:11 AM, Rui Oliveira > <rui18oliver at gmail.com> wrote: >> Good afternoon. >> >> I am a master student in University of Porto in Portugal. At this >> moment I?m >> starting to use R, so I have some doubts. >> >> The aim of my analysis is: calculate a pairwise FST matrix from >> fasta file >> and creat a principal component analyses with adegenet package (I >> use seqinr >> and ape package to read this file, then I convert this file into a >> genind >> object with DNA2genind function provide in adegenet package). After >> convert >> my file the pairwise.fst function is not found. >> >> If you could help me would be great. >> >> Greetings: Rui OliveiraDavid Winsemius, MD West Hartford, CT
On Jul 28, 2011, at 11:54 AM, David Winsemius wrote:>> On Thu, Jul 28, 2011 at 8:11 AM, Rui Oliveira >> <rui18oliver at gmail.com> wrote: >>> Good afternoon. >>> >>> I am a master student in University of Porto in Portugal. At this >>> moment I?m >>> starting to use R, so I have some doubts. >>> >>> The aim of my analysis is: calculate a pairwise FST matrix from >>> fasta file >>> and creat a principal component analyses with adegenet package (I >>> use seqinr >>> and ape package to read this file, then I convert this file into a >>> genind >>> object with DNA2genind function provide in adegenet package). >>> After convert >>> my file the pairwise.fst function is not found.That suggests a problem in loading the adegenet package. You should post a copy of your console transcript and post sessionInfo() ... as is requested in the Posting Guide.>>> >>> If you could help me would be great. >>> >>> Greetings: Rui OliveiraSorry for the blank message. Meant to come back to edit it. David Winsemius, MD West Hartford, CT