[GenABEL-dev] ld-based pruning

[L.C. Karssen]

Hi Yurii,

That's an excellent suggestion. This makes me more inclined to put
Paul's function in GenABEL. Most users already have that package
installed and if we would make separate ProbABEL-R-tools package it
would mean yet another package people need to install and keep up to
date on their systems.

The only thing that remains in terms of input checking is a check for
the existence of the ProbABEL config file. But that's easy.


Lennart.

On 20/03/13 12:00, Yurii Aulchenko wrote:
> 
>     Technically, if we make it part of GenABEL would that mean that GenABEL
>     depends on DatABEL (now it is only a suggested dependency) since Paul's
>     function 'require()'s DatABEL? Are there any other R packages that have
>     functionality that only works if a given package is installed (that is
>     not in the dependency list but only in the suggested list)?
> 
> 
> 
> I do not see a big problem with above - e.g. there are functions like
> minimac2databel in the GenA. They start with
> (https://r-forge.r-project.org/scm/viewvc.php/pkg/GenABEL/R/minimac2databel.R?view=markup&root=genabel)
> 
> minimac2databel <- function(imputedgenofile, infofile, outfile, cachesizeMb=64)
> {
>   if (!require(DatABEL))
>     stop("This function requires DatABEL package to be installed")
> 
> 
> This seems to be accepted practice
> 
> Yurii

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L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org

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