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Dave, Greg, Ross and Scott teleconferred on March 9
- Of note: Ross invited to given an Rgenetics talk at BioC2007?, Seattle August 6&7 with a Developer's day on August 8. UseR in Ames, Iowa (Dave is on the organizing committee) August 9,10 and 11.
- Alpha: Fbat, GeneticsBase and GeneticsDesign? now in the BioC developer repository. GeneticsPed now passes check and build tests and has rudimentary vignettes. Dave will notify Herve of the availability of GeneticsPed. R2VCE status not known - Gregor?
- Plink: Greg will spend more time spelunking the source at http://pngu.mgh.harvard.edu/~purcell/plink/index.shtml and will report on wrapper developments. Internal representation not yet clarified. Ross has a bunch of scripts for generating QC report web pages in python and R from Plink runs over large whole genome data sets available if anyone wants them.
- SNPHap: Despite the savings of RAM over integer matrices, Vince expressed some uneasiness at the use of raw mode matrices on account of the difficulty of ensuring that book-keeping was perfect in terms of all accessor functions. Greg suggested that these could be made more verifiable in C. Ross noted that Weiliang had tested plink and snphap for consonance on small data sets and got the same allele counts and hwe stats. Ross to checkin the latest SNPMatrix code to our svn so we can annotate it as we study it.
- SNPChip: Greg mentioned another SNP package on BioC dev. Ross found http://bioconductor.org/packages/2.0/bioc/vignettes/SNPchip/inst/doc/SNPchip.pdf but it's primarily devoted to CNV studies using affy snpchips. Uses eSet as representation...
- Scott's volunteer helper: First project for will be writing a QC harness. Second could be Plink wrappers?
- Rgenetics meetings: Ross has budgetted some money for developer meetings. Will discuss with Vince. Dave pointed out that BioC developer days are generally fairly low key events without a lot of structure. Greg and Ross could go; Dave maybe for half a day; Scott not likely available on August 8. Perhaps early 2008?
- Next telecon: March 23 2007, 1:30 pm EST