[R-sig-genetics] R-sig-genetics Digest, Vol 8, Issue 2

Sat Sep 11 01:54:46 CEST 2010

Hi Ross,

Thanks for this.  I take it then that the QC tools you have in Galaxy 
are not in any of the Bioconductor Genetics{Base,Design,Ped} packages? 
If not, are there plans to update the Bioconductor packages?

Cheers,

Brad
---
Brad McNeney
Statistics and Actuarial Science
Simon Fraser University

On 10/09/2010 11:51 AM, Ross wrote:
> Hi, Fernando,
>
> I think there are some QC tools in David Clayton's snpMatrix package,
> but there's no single R package to do all the reports you need AFAIK.
> For comprehensive reporting, if you don't mind not using R, one option
> is to try the SNP/WGA tools in Galaxy - they do use R for graphics but
> you don't need to install anything as it all works through an ordinary
> web browser.
>
> Essentially, if you have your genotype and pedigree data in Plink
> style linkage format (separate map and ped files), the steps are
> something like this:
>
> 1. make yourself a new user account at the main Galaxy server
> (http://usegalaxy.org) so your histories are preserved between logins
>
> 2. From the analysis window, left (tool) pane, click the Get Data tool
> group header to expand the group, then click the 'upload file' tool.
> A form will appear in the center pane of your browser.
>
> 3. Change the file format (first field on the form) from Auto to
> "lped" format as autodetect won't work for these multi-part datatypes
> 4. Make the 'ped' and 'map' file upload fields point to the right map
> and ped files on your local machine, set the 'build' to hg18 and
> change the name to reflect something informative about your data then
> click execute.
>
> 5. After the data are uploaded (should only take a minute or two for a
> small file) to your history, you can select the SNP/WGA QC LD Plots
> tool submenu in the tool pane and then click the QC tool. Another form
> will open in the center panel. Your new dataset should be the only one
> available in the drop-down list of files to process. Change the QC job
> name to a meaningful name, click 'execute'. For a small dataset, the
> whole process should run for a few minutes but you can safely log out
> and log back in later - your work will all be preserved.
>
> 6. The QC tool output (in the right side history pane) has an 'eye'
> icon which you can click to open up the report in the center panel -
> you should see HWE/missingness/Mendel and all sorts of other useful
> plots and there are some tabular files containing summary details by
> marker and by sample.
>
> I'm happy to answer any questions you might have - I hope this helps
> get you started?
>
> There's a 'clean' tool you can use to remove markers and subjects that
> fall below specific thresholds for QC measures and there's a TDT tool
> you can use for analysis of family data.
>
>
> On Fri, Sep 10, 2010 at 6:00 AM,<r-sig-genetics-request at r-project.org>  wrote:
>> Send R-sig-genetics mailing list submissions to
>>         r-sig-genetics at r-project.org
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>>         https://stat.ethz.ch/mailman/listinfo/r-sig-genetics
>> or, via email, send a message with subject or body 'help' to
>>         r-sig-genetics-request at r-project.org
>>
>> You can reach the person managing the list at
>>         r-sig-genetics-owner at r-project.org
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of R-sig-genetics digest..."
>>
>>
>> Today's Topics:
>>
>>    1. Available R packages to QC/summarize large SNP    datasets?
>>       (GRIGNOLA, FERNANDO E [AG/1000])
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Thu, 9 Sep 2010 10:54:23 -0500
>> From: "GRIGNOLA, FERNANDO E [AG/1000]"
>>         <fernando.e.grignola at monsanto.com>
>> To:<r-sig-genetics at r-project.org>
>> Subject: [R-sig-genetics] Available R packages to QC/summarize large
>>         SNP     datasets?
>> Message-ID:
>>         <2335BBF3D6579746A3165D5D7B95DF7018D1BB at NA1000EXM12.na.ds.monsanto.com>
>>
>> Content-Type: text/plain; charset="us-ascii"
>>
>> Hi,
>>
>> I looking for some guidance regarding available packages to do QC (i.e.
>> parent-offspring inheritance checks) and to summarize large SNP datasets
>> (i.e. 50K) for pedigreed populations (frequencies, linkage calculations,
>> etc).
>>
>> I know of some packages that check for HW equilibrium, get frequencies
>> as part of the data preparation for genome-wide association analyses for
>> example. However, I was wondering if somebody can point me to 1 or 2
>> packages that mostly focus on data quality and summary statistics for
>> large SNPs of data.
>>
>> Thanks in advance for your assistance,
>>
>>
>>
>> Fernando
>>
>>
>>
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL:<https://stat.ethz.ch/pipermail/r-sig-genetics/attachments/20100909/79833d2b/attachment-0001.html>
>> -------------- next part --------------
>>
>> This e-mail message may contain privileged and/or confidential information, and is intended to be received only by persons entitled to receive such information. If you have received this e-mail in error, please notify the sender immediately. Please delete it and all attachments from any servers, hard drives or any other media. Other use of this e-mail by you is strictly prohibited.
>>
>> All e-mails and attachments sent and received are subject to monitoring, reading and archival by Monsanto, including its subsidiaries. The recipient of this e-mail is solely responsible for checking for the presence of "Viruses" or other "Malware". Monsanto, along with its subsidiaries, accepts no liability for any damage caused by any such code transmitted by or accompanying this e-mail or any attachment.
>>
>>
>> The information contained in this email may be subject to the export control laws and regulations of the United States, potentially including but not limited to the Export Administration Regulations ("EAR") and sanctions regulations issued by the U.S. Department of Treasury, Office of Foreign Asset Controls (?OFAC?).  As a recipient of this information you are obligated to comply with all applicable U.S. export laws and regulations.
>>
>> ------------------------------
>>
>> _______________________________________________
>> R-sig-genetics mailing list
>> R-sig-genetics at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-genetics
>>
>>
>> End of R-sig-genetics Digest, Vol 8, Issue 2
>> ********************************************
>>
>
>
>