Hi, I want to analyse DNA sequence data (mtDNA) in R as in calculate Fst, Heterozygosity and such summary statistics. Package Adagenet converts the DNA sequence into retaining only retaining the polymorphic sites and then calcuates Fst.. but is there any other way to do this? I mean analyse the DNA sequence as it is.. and calculate the statistics? Thanks! [[alternative HTML version deleted]]
Hello Blue Ray, I have worked with DNA, but frankly I do not know what Fst, Heterozygosity and "such summary statistics" might be. If you could explain a little, maybe even give a reference about their meaning and how to do the calculations, people who are not biologists but know R might be able to give you advice, increasing the probability of being answered :-) Tim On Mon, Aug 23, 2010 at 12:30:28PM +0200, blue jay wrote:> Hi, > > I want to analyse DNA sequence data (mtDNA) in R as in calculate Fst, > Heterozygosity and such summary statistics. Package Adagenet converts the > DNA sequence into retaining only retaining the polymorphic sites and then > calcuates Fst.. but is there any other way to do this? I mean analyse the > DNA sequence as it is.. and calculate the statistics? > > > Thanks! > > [[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.-- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 189 bytes Desc: Digital signature URL: <https://stat.ethz.ch/pipermail/r-help/attachments/20100823/a3bdb6de/attachment.bin>
Hi,
Take a look at the Bioconductor packages, particularly "BSgenome". If
that isn't specific enough, you might want to try the Bioconductor
mailing list rather than "R-help".
http://www.bioconductor.org/packages/release/bioc/html/BSgenome.html
bioconductor at stat.math.ethz.ch
Best regards,
Charlie Roosen
Mango Solutions
-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
On Behalf Of blue jay
Sent: 23 August 2010 12:30
To: r-help at r-project.org
Subject: [R] DNA sequence Fst
Hi,
I want to analyse DNA sequence data (mtDNA) in R as in calculate Fst,
Heterozygosity and such summary statistics. Package Adagenet converts
the
DNA sequence into retaining only retaining the polymorphic sites and
then
calcuates Fst.. but is there any other way to do this? I mean analyse
the
DNA sequence as it is.. and calculate the statistics?
Thanks!
[[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.
LEGAL NOTICE
This message is intended for the use o...{{dropped:9}}
Hi Blue Jay, If your sequences are small (<10Kb) and you have a few samples (~100) the seqinr package from CRAN itself is a very straightforward way of handling DNA sequences, but if you plan to do more sophisticated things that can drain your RAM and processor time, I would definitely recommend the more versatile but complex Biostrings package from Bioconductor. www.bioconductor.org/packages/2.2/bioc/html/*Biostrings*.html Happy DNARing! Keo. El 23/08/10 05:30 a.m., blue jay escribi?:> Hi, > > I want to analyse DNA sequence data (mtDNA) in R as in calculate Fst, > Heterozygosity and such summary statistics. Package Adagenet converts the > DNA sequence into retaining only retaining the polymorphic sites and then > calcuates Fst.. but is there any other way to do this? I mean analyse the > DNA sequence as it is.. and calculate the statistics? > > > Thanks! > > [[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.