Hello, I hoped you could help. The original querry is: >> We are now looking for a prior step that can convert our data into >> population frequencies. The data we have are in SNP frequencies and >> the >> format of the data are >> >> ind1 ind2 ind3 ind4 >> Loc1 AA AC CC AC >> Loc2 CC CT -- CT >> >> And so on. We need to preprocess so that we select which columns >> from which >> populations. We also need to interpret the genotypes correctly (and >> note >> that -- is missing data). >> >> Do you know of any R routines that can do this? Does APE have this >> functionality? The data are from the Illumina beadstation SNP caller. I see that bioconductor can call SNP's from the raw data, but I did not see a link to the follow up we need prior to estimating genetic distances of populations. Thanks, Peter. On 5/18/10 2:24 PM, "Brian O'Meara" <omeara.brian at="" gmail.com=""> wrote: > Hi, Peter. I don't know what can do what you want (I'd be tempted to > write something treating the input data as factors). I don't think APE > can do this. However, you should look at http://www.bioconductor.org > -- it has a set of 389 packages for genomic analysis, several of which > deal with SNP data (there are even packages for processing raw tiff > data from Illumina beadarrays > (<http: www.bioconductor.org="" packages="" release="" bioc="" html="" beadarray.h="" tml="">> )). You might also look at the Genetics task view for relevant > packages (<http: cran.r-project.org="" web="" views="" genetics.html="">) > > Hope this helps, > Brian > > On May 18, 2010, at 2:09 PM, Waddell, Peter J wrote: > >> Hello, >> >> Could you please help me to contact Daniel and/or help answer the >> questions >> below. >> >> Many thanks, >> >> Peter. >> >> >> ------ Forwarded Message >> From: "Waddell, Peter J" <pwaddell at="" purdue.edu=""> >> Date: Mon, 17 May 2010 18:06:11 -0400 >> To: "chessel at biomserv.univ-lyon1.fr" <chessel at="" biomserv.univ-="" lyon1.fr=""> >> Cc: "khan27 at purdue.edu" <khan27 at="" purdue.edu=""> >> Subject: R functions for genetic distances >> >> Dear Daniel, >> >> We were very pleased to find your R routines to calculate genetic >> distances >> in R, in particular, Nei's, Reynold et al. etc. distances. >> >> We are now looking for a prior step that can convert our data into >> population frequencies. The data we have are in SNP frequencies and >> the >> format of the data are >> >> ind1 ind2 ind3 ind4 >> Loc1 AA AC CC AC >> Loc2 CC CT -- CT >> >> And so on. We need to preprocess so that we select which columns >> from which >> populations. We also need to interpret the genotypes correctly (and >> note >> that -- is missing data). >> >> Do you know of any R routines that can do this? Does APE have this >> functionality? The data are from the Illumina beadstation SNP caller. >> >> Many thanks, >> >> Peter Waddell. >> >> >> On 5/17/10 5:28 PM, "khan27 at purdue.edu" <khan27 at="" purdue.edu=""> wrote: >> >>> >>> functions : >>> genet.html >>> dist.genet >>> >>> Author: >>> Daniel Chessel chessel at biomserv.univ-lyon1.fr >>> >>> Link: >>> http://pbil.univ-lyon1.fr/ade4html/ >>> >>> Thanks, >>> >>> Ishita >> >> >> ------ End of Forwarded Message >> > > ------------------------------------------------------ > Brian O'Meara > http://www.brianomeara.info > Assistant Prof. > Dept. Ecology & Evolutionary Biology > U. of Tennessee, Knoxville >