Re: [R-sig-phylo] Does anyone know about a function to remove redundancy from a database?
Hi, Or use haplotype() in pegas. Emmanuel -Original Message- From: Klaus Schliep Sender: r-sig-phylo-boun...@r-project.org Date: Tue, 19 Feb 2013 15:15:13 To: Luiz Max Carvalho Cc: Subject: Re: [R-sig-phylo] Does anyone know about a function to remove redundancy from a database? Hi Luiz, phangorn has a generic unique function for phyDat objects. There may be more elegant ways, but this code should work: library(phangorn) y = as.DNAbin(unique(as.phyDat(x))) Cheers, Klaus On 2/19/13, Luiz Max Carvalho wrote: > I've been looking for a function that could scan a DNAbin object and return > just the unique sequences. Does anyone know about a function for that? > > Thanks in advance, > > -- > Luiz Max Fagundes de Carvalho, IC, Programa de Computação Científica > (PROCC), Fundação Oswaldo Cruz, Rio de Janeiro, Brasil. > https://www.researchgate.net/profile/Luiz_Fagundes_de_Carvalho/?ev=prf_info > > [[alternative HTML version deleted]] > > -- Klaus Schliep Phylogenomics Lab at the University of Vigo, Spain ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] Does anyone know about a function to remove redundancy from a database?
Great! Thank you! 2013/2/19 Klaus Schliep > Hi Luiz, > > phangorn has a generic unique function for phyDat objects. > There may be more elegant ways, but this code should work: > library(phangorn) > y = as.DNAbin(unique(as.phyDat(x))) > > Cheers, > Klaus > > > On 2/19/13, Luiz Max Carvalho wrote: > > I've been looking for a function that could scan a DNAbin object and > return > > just the unique sequences. Does anyone know about a function for that? > > > > Thanks in advance, > > > > -- > > Luiz Max Fagundes de Carvalho, IC, Programa de Computação Científica > > (PROCC), Fundação Oswaldo Cruz, Rio de Janeiro, Brasil. > > > https://www.researchgate.net/profile/Luiz_Fagundes_de_Carvalho/?ev=prf_info > > > > [[alternative HTML version deleted]] > > > > > > > -- > Klaus Schliep > Phylogenomics Lab at the University of Vigo, Spain > -- Luiz Max Fagundes de Carvalho, IC, Programa de Computação Científica (PROCC), Fundação Oswaldo Cruz, Rio de Janeiro, Brasil. https://www.researchgate.net/profile/Luiz_Fagundes_de_Carvalho/?ev=prf_info [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] Does anyone know about a function to remove redundancy from a database?
Hi Luiz, phangorn has a generic unique function for phyDat objects. There may be more elegant ways, but this code should work: library(phangorn) y = as.DNAbin(unique(as.phyDat(x))) Cheers, Klaus On 2/19/13, Luiz Max Carvalho wrote: > I've been looking for a function that could scan a DNAbin object and return > just the unique sequences. Does anyone know about a function for that? > > Thanks in advance, > > -- > Luiz Max Fagundes de Carvalho, IC, Programa de Computação Científica > (PROCC), Fundação Oswaldo Cruz, Rio de Janeiro, Brasil. > https://www.researchgate.net/profile/Luiz_Fagundes_de_Carvalho/?ev=prf_info > > [[alternative HTML version deleted]] > > -- Klaus Schliep Phylogenomics Lab at the University of Vigo, Spain ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
[R-sig-phylo] Does anyone know about a function to remove redundancy from a database?
I've been looking for a function that could scan a DNAbin object and return just the unique sequences. Does anyone know about a function for that? Thanks in advance, -- Luiz Max Fagundes de Carvalho, IC, Programa de Computação Científica (PROCC), Fundação Oswaldo Cruz, Rio de Janeiro, Brasil. https://www.researchgate.net/profile/Luiz_Fagundes_de_Carvalho/?ev=prf_info [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
