Hi, if anyone else (especially Linux users) would have similar problem with GIT and/or zipped package, this is the issue https://github.com/hadley/devtools/issues/406 It also contains useful link how to solve it. Basically, set unzip command in appropriate R option or download zip, unzip it at package as tar.gz and install manually. Linarius looks like very interesting package, but unfortunately only for dominant data... All the best, V.
Dne Po 9. června 2014 16:19:09 jste napsal(a): > Hi, > it isn't in cran yet, right? I'm not able to install it from the zip (master > branch from git): > install.packages(file.choose(), repos=NULL, lib.loc="~/R/x86_64-suse-linux- > gnu-library/3.1/", instlib="~/R/x86_64-suse-linux-gnu-library/3.1/") > Installing package into ‘/home/vojta/R’ > (as ‘lib’ is unspecified) > Error in rawToChar(block[seq_len(ns)]) : > embedded nul in string: > 'PK\003\004\n\0\0\0\0\0m\x94\x8bD\0\0\0\0\0\0\0\0\0\0\0\0\020\0\t\0Linarius- > master/UT\005\0\001_\x98HSPK\003\004\n\0\0\0\b\0m\x94\x8bD\x8ewq\xa1\030\0\ > 0\0\034\0\0\0\035\0\t\0Linarius- master' > Warning message: > In install.packages(file.choose(), repos = NULL, lib.loc = "~/R/x86_64-suse- > linux-gnu-library/3.1/", : > installation of package ‘/home/vojta/plocha/Linarius-master.zip’ had non- > zero exit status > I'm using Linux if it matters. Honestly, I have no idea, what this error > means... > All the best, > Vojtěch > > Dne Pá 30. května 2014 13:39:14 jste napsal(a): > > Hi, > > > > I'm also curently developing a R package: > > https://github.com/giby/Linarius that can be used for triploid… actually > > it > > is designed for mixed ploidy levels. But right now, I focus on AFLP. As I > > told you there is much more thing availlable for microsatelites. Benjamin > > > > Le Vendredi 30 Mai 2014 09:17 GMT, Vojtěch Zeisek <[email protected]> a écrit: > > > Hello, > > > thank You both. poppr looks interesting, I need to explore it more. > > > Adegenet is famous package. I didn't know it can also handle triploid > > > data. I found problem when importing data to it. Functions of > > > import2genind group (read.genetix, read.structure, read.fstat and > > > read.genepop) are only for diploid data. So I used read.loci. The input > > > file was easy: first line with names of markers etc, first row with > > > names > > > of samples, second row with populations and from third row alleles. I > > > coded alleles in this way 123/234/345, so that each individual has 3 > > > alleles. Missing alleles are just NA. > > > ssrs3n.loci <- read.loci("ssrs3n.txt", header=TRUE, loci.sep="\t", > > > allele.sep="/", col.pop=2, col.loci=3:10, row.names=1) ssrs3n.loci > > > Allelic data frame: 130 individuals > > > > > > 8 loci > > > 1 additional variable > > > > > > ssrs3n.genind <- loci2genind(ssrs3n.loci) > > > ssrs3n.genind > > > > > > ##################### > > > ### Genind object ### > > > ##################### > > > > > > - genotypes of individuals - > > > > > > S4 class: genind > > > @call: df2genind(X = as.matrix(x[, attr(x, "locicol")]), sep = "/", > > > > > > pop = pop) > > > > > > @tab: 130 x 115 matrix of genotypes > > > > > > @ind.names: vector of 130 individual names > > > @loc.names: vector of 8 locus names > > > @loc.nall: number of alleles per locus > > > @loc.fac: locus factor for the 115 columns of @tab > > > @all.names: list of 8 components yielding allele names for each locus > > > @ploidy: 2 > > > @type: codom > > > > > > Optional contents: > > > @pop: factor giving the population of each individual > > > @pop.names: factor giving the population of each individual > > > > > > @other: - empty - > > > > > > As You can see, it was imported as diploid and I haven't found way how > > > import it as triploid data. Imported data matrix seems to be wrong. When > > > I used input file formatted in the same way for diploids, it works > > > perfectly... Any ideas how to fix that? > > > Thank You in advance, > > > Vojtěch Zeisek > > > > > > Dne Pá 30. května 2014 03:34:49 jste napsal(a): > > > > Hi there, > > > > > > > > yes, adegenet handles any (constant) ploidy for most purposes. For > > > > input > > > > formats etc. please see the tutorial on basics, section 'documents' > > > > on: > > > > http://adegenet.r-forge.r-project.org/ > > > > > > > > Please feel free to use the adegenet forum for adegenet-related > > > > questions. > > > > Cheers > > > > Thibaut > > > > > > > > ________________________________________ > > > > From: [email protected] > > > > [[email protected]] > > > > on behalf of Gilles Benjamin Leduc [[email protected]] Sent: 29 May 2014 > > > > 17:12 > > > > To: Vojtěch Zeisek > > > > Cc: mailinglist R > > > > Subject: Re: [R-sig-phylo] Triploid microsatellites? > > > > > > > > Hi, > > > > > > > > Yes it is possible in R, there is a package created for related > > > > purposes: > > > > poppr or something like that… The dev version on github should be > > > > preferred. I have seen several R work with polyploids and > > > > microsatelites, > > > > unfortunately… I work with ALFP :p Benjamin > > > > > > > > Le Jeudi 29 Mai 2014 13:40 GMT, Vojtěch Zeisek <[email protected]> a écrit: > > > > > Hello, > > > > > I wonder if it is possible to handle triploid microsatellite (yes, > > > > > all > > > > > individuals are regular 3n) data in adegenet and another R packages. > > > > > And > > > > > if so, how to enter the data. Any experiences and/or Ideas are very> > > > > > > > > > > > welcomed. :-) Structure and BAPS are working well. Yours sincerely, > > > > > Vojtěch Zeisek -- Vojtěch Zeisek http://trapa.cz/en/ Department of Botany, Faculty of Science Charles University in Prague Benátská 2, Prague, 12801, CZ http://botany.natur.cuni.cz/en/ Institute of Botany, Academy of Science Zámek 1, Průhonice, 25243, CZ http://www.ibot.cas.cz/en/ Czech Republic
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