[BioC] strange behavior with hsahomology

[Francois Pepin]

Hi everyone,

I've been playing with the hsahomology package and gone through the
vignette and there is something I don't understand.

Sometimes it seems the scores are in homoURL instead of homoPS. It seems
like a bug to me, or is it a feature I don't understand?

> homo <- unlist(as.list(hsahomologyDATA))
 #one arbitrary case where this is the case
> x<-grep("396050", homo)
> as.matrix(homo[(x-2):(x+2)])
                   [,1]    
6337.9031.homoOrg  "gga"   
6337.9031.homoType "m"     
6337.9031.homoHGID "396050"
6337.9031.homoPS   NA      
6337.9031.homoURL  "66.84" 

There seems to be a lot of cases where this happens, and it would seem
to me that most of the code using those scores would be rather confused
by this.

> sessionInfo()
R version 2.4.0 Patched (2006-10-03 r39576) 
i386-apple-darwin8.8.1 

locale:
C

attached base packages:
[1] "methods"   "stats"     "graphics"  "grDevices" "utils"
"datasets" 
[7] "base"     

other attached packages:
hsahomology 
   "1.14.0" 

Francois