User: Voke AO

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Voke AO760
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Posts by Voke AO

<prev • 76 results • page 1 of 8 • next >
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Plink Data for Fst Calculations
... Hi all, Are there any bioconductor packages besides snpStats that can directly use plink data format for Fst calculations? Any response will be greatly appreciated. Regards. Avoks [[alternative HTML version deleted]] ...
snpstats written 4.0 years ago by Voke AO760
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Comment: C: Formatting in R
... Thank you Stephanie. -Avoks On Thu, Oct 3, 2013 at 8:28 PM, Stephanie M. Gogarten < sdmorris@u.washington.edu> wrote: > Hi Avoks, > > This is more of an R-help question than a Bioconductor question, but > here's something that I think will work for you. Step 1 does some indexi ...
written 4.1 years ago by Voke AO760
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Formatting in R
... Hi all, I have two files I need to merge but first I need to reformat one of them...it looks like this: GENE1 snp001 snp002 snp003 snp004 END GENE2 snp005 snp006 snp007 snp008 END GENE3 snp009 snp010 snp011 snp012 END It's pretty much a set file from Plink. What I'd like to do is to have the ...
written 4.1 years ago by Voke AO760 • updated 4.1 years ago by Stephanie M. Gogarten530
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snpStats Fst Implementation
... Hi all, I couldn't find anywhere I could read up on which of the Fst implementations the snpStats package uses...Weir and Cockerham? Also, what does it mean when there are NAs in some rows of the Fst column? Any input will be greatly appreciated. Thanks Avoks [[alternative HTML version ...
snpstats written 4.2 years ago by Voke AO760
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SnpStats - STRING_ELT() error and Fst
... Hi all, I was attempting to calculate Fst on some 1000 genomes data in binary plink format but I encountered this error below and I'm not quite sure how to get around it. Any suggestions will be greatly appreciated. Thanks Avoks > MySample=read.plink("MyAFR_Plus") > MyAttrib = read.delim(" ...
genomes written 4.2 years ago by Voke AO760
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Answer: A: Fst Calculation Packages
... Thanks Vincent. I googled as well...should have done that in the first place. Thanks again. -Avoks On Wed, Aug 21, 2013 at 2:41 PM, Vincent Carey wrote: > See the function Fst in the snpStats package, for one example. > > > On Wed, Aug 21, 2013 at 4:24 AM, Ovokeraye Achinike-Oduaran ...
written 4.3 years ago by Voke AO760
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Fst Calculation Packages
... Hi, Can I please get suggestions of packages to use for Fst calculations within and across populations? Thanks and regards, Avoks [[alternative HTML version deleted]] ...
written 4.3 years ago by Voke AO760
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Comment: C: rs ids Retrieval using biomaRt
... Thanks Vincent. The original code actually was alright. The problem was with my input file...it had to be colon (:)-separated. Thanks again. Regards, Avoks On Sat, Nov 3, 2012 at 3:03 PM, Vincent Carey wrote: > arrange for the start and end coordinates to be numerical vectors. how you > ...
written 5.1 years ago by Voke AO760
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Comment: C: rs ids Retrieval using biomaRt
... Thanks Vincent. You are right about the filters. One more thing: how would this work with a batch input "values" list i.e reading the positions from a file? For example: CHR 1, 11182261, 11182261 1, 11264032, 11264032 1, 11264036, 11264036 1, 11282246, 11282246 1, 11292945, 11292945 1, 11306660, 11 ...
written 5.1 years ago by Voke AO760
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rs ids Retrieval using biomaRt
... Hi all, I've been trying to retrieve SNP rsids using biomaRt for a number of SNPs where I have their positions. My input file looks like this: 1 888899000 888899000 where, 1 = chromosome number and the second and third numbers are the position of the SNP. My code looks like this: library(biomaR ...
snp biomart written 5.1 years ago by Voke AO760 • updated 5.1 years ago by Vincent J. Carey, Jr.6.2k

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