Minutes for 2007-10-12

In Attendance: Greg, Ross, Nitin, Scott

Note taker for today: Greg

Status of our packages in latest BioC build:

Greg: The announcement said GeneticsPed didn't make it into the 2.1 release. The build-report for 2.2 shows:

> ### * datasets
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: Mrode
> ### Title: Pedigree and data examples
> ### Aliases: Falconer Falconer5.1 Mrode Mrode2.1 Mrode3.1
> ### Keywords: datasets
> 
> ### ** Examples
> 
>   data(Falconer5.1)
>   Pedigree(x=Falconer5.1, id="sub", ascendant=c("fat", "mot"))

Error in Pedigree(x = Falconer5.1, id = "sub", ascendant = c("fat", "mot")) : unused argument(s) (id = "sub")

Greg sent an email to Dave Henderson about this.

In the BioC 2.2 build, we have a problem with $ being used for non-list components. Ross will ask Weiliang to look at this.:

> ###
> # Generate a LaTeX Linkage Disequilibrium table
> ###
> ld <- LD(CAMP)
> # display inline
> latex(ld, filename="")

Error in x$footer : $ operator not defined for this S4 class Calls: latex ... latex -> .local -> xtable -> xtable.data.frame -> gsub Execution halted

To Do:

• We need to sit down and look at the list of desired features, and compare with the list of features that are complete.

  Nitin: Go through man pages and make a list of what features

  are present, and any features that are obviously missing.

  Next meeting we'll review the list and add our own elements.

• We also need to 'bang on it' some more.

Key Features:

For Ross: efficiency with large data sets (500K SNPS NOW, 1M next year)

• implement the more efficient SNP storage classes

  need: vector/matrix code for handling 2-bit representation

  0,1,2 copies + NA

  perhaps we can use the implementation in boost: The Boost C++ Libraries provides a dynamic_bitset class whose size is specified at run-time. Details at: http://www.boost.org/libs/dynamic_bitset/dynamic_bitset.html