[BioC] GWATools use in creating ncdf files

[Stephanie M. Gogarten]

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).

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>
>