Hi. On Thu, Mar 17, 2011 at 1:39 PM, Herbeck <joshherb...@gmail.com> wrote: > Hi, > > Is there a way for aroma to output genotype calls into a standard > format, like .ped/.map?
Sorry, there is nothing out of the box for this. As illustrated in the 'CRLMM genotyping (100K and 500K)' vignette [http://aroma-project.org/vignettes/CRLMM100K500K], you can quite easily access the genotype calls per sample or across the whole set for all or for a subset of the SNPs using the extractGenotypes() method(s). Beyond that there is nothing much, but it provides the basics for exporting genotype calls to other file formats. Not sure what's available from Bioconductor; maybe there are some export functions that you can utilize in combination with this. Feel free to share with us if you learn something useful. Also, there is no data structures in the aroma framework for representing pedigrees, which means that there is really nothing to export in that sense. /Henrik FOR FUTURE REFEFENCES ONLY: See http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml for these file formats (PED, MAP, Binary PED). > > Thanks a lot! > > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
