[BioC] GWATools use in creating ncdf files

[Stephanie M. Gogarten]

GWASTools versions 1.6.2 (release) and 1.7.4 (devel) have better error 
messages in anomDectectBAF that may help diagnose where your error is 
occurring.  These versions will be available through biocLite() tomorrow 
after ~10am Pacific time (or right now via svn).  If you haven't figured 
it out already, try upgrading and report what error message you get.

Stephanie

On 5/30/13 1:43 PM, Stephanie M. Gogarten wrote:
> Hi Sam,
>
> I need to add a more informative error message - the problem is that no
> valid BAF values are reaching the call to CNA (baf.dat is NULL).  This
> could happen if the values of snp.ids or chrom.ids are invalid - these
> should all be integer values matching the contents of snpID and
> chromosome in the netCDF file.  What values are you using for these
> arguments?
>
> You will need to have LRR in the intensity NetCDF file.  A portion of
> the code downstream from the error you're getting uses LRR to filter
> potential anomalies.
>
> Stephanie
>
> On 5/30/13 12:30 PM, Sam Rose wrote:
>> Thank you for your previous help Stephanie.
>>
>> I am afraid I have another problem I can't seem to work out.
>>
>> I have gotten as far as reading in the BAlleleFreq and Geno files into
>> their respective ncdf formats. I only have the baf data in the intensity
>> ncdf file, do I need LRR too? When I run the anomDetectBAF() function it
>> gives me this error:
>>
>>  > anom <- anomDetectBAF(blData, genoData, scan.ids=scan.ids,
>> chrom.ids=chrom.ids, snp.ids=snp.ids, centromere=centromeres.hg19)
>> Error in CNA(as.vector(baf.dat), chr, index, data.type = "logratio",
>> sampleid = snum) :
>>    genomdat must be numeric
>>
>> I have checked and the data that I put in to the genotype data file was
>> numeric and present as well as the baf data. I'm wondering if you have
>> seen this error before and may potentially know what I can do to rectify?
>>
>> Thanks,
>> Sam
>>
>>
>> On Wed, Apr 24, 2013 at 12:01 AM, Stephanie M. Gogarten
>> <sdmorris at u.washington.edu <mailto:sdmorris at u.washington.edu>> wrote:
>>
>>     Hi Sam,
>>
>>     Section 2 of the vignette "GWAS Data Cleaning" contains an example
>>     of how to import raw illumina data of exactly this type into
>>     GWASTools. The example data is contained in the package "GWASdata."
>>
>>     If you have any further questions after reading the vignette, please
>>     cc the bioconductor mailing list (bioconductor at r-project.org
>>     <mailto:bioconductor at r-project.org>).
>>
>>     Section 7 may also be of use to you, as it deals with chromosome
>>     anomaly detection.
>>
>>     best wishes,
>>     Stephanie
>>
>>
>>     On 4/23/13 7:54 PM, Sam Rose wrote:
>>
>>         Hi Stephanie,
>>
>>         My name is Sam Rose and I am contacting you the GWASTools
>> package in
>>         Bioconductor of which it says you are the maintainer.
>>
>>         I am trying to use the package to call mosaic CNVs in my
>> samples and
>>         can't seem to get it to work.
>>
>>         I'm wondering if you have an example of the raw illumina data to
>>         put in
>>         there, and maybe examples of some of the things required in the
>>         'ncdfAddData' command (i.e. sample column, col.nums). I have
>>         created the
>>         shell ncdf file, but beyond that the headers and data formats
>>         seem to be
>>         giving me trouble so I just though I would ask.
>>
>>         Our Illumina raw data files look like this:
>>
>> SNP_NameChromosomePositionGC___ScoreAllele1_-_TopAllele2_-___TopAllele1_-_ABAllele2_-___ABXYRaw_XRaw_YR_IlluminaTheta___IlluminabAllele_FreqLog_R___Ratio_IlluminaR_TrigTheta___TrigLog_R_Ratio_Trig
>>
>>
>> rs44772121720170.__38423407AAAA0.__393692269026780450.__0250181864147452338333240.__41871045544152570.__040401312884379780.__006063504097364059-0.__6120798296992830.__394486390567453940.__06346223387647508-0.__6182450719587295
>>
>>
>>         Thanks for your help,
>>
>>         Sam
>>
>>         --
>>         -----
>>         *Sam Rose, Stanley Center Research Associate II
>>
>>         Stanley Center for Psychiatric Research, The Broad Institute
>>         7 Cambridge Center, Cambridge, MA 02142*
>>         617.714.7853, srose at broadinstitute.org
>>         <mailto:srose at broadinstitute.org>
>>         <mailto:srose at broadinstitute.__org
>>         <mailto:srose at broadinstitute.org>>
>>
>>
>>
>>
>> --
>> -----
>> *Sam Rose, Stanley Center Research Associate II
>> Stanley Center for Psychiatric Research, The Broad Institute
>> 7 Cambridge Center, Cambridge, MA 02142*
>> 617.714.7853, srose at broadinstitute.org <mailto:srose at broadinstitute.org>
>>
>
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