[BioC] strange behavior with hsahomology

Francois Pepin fpepin at cs.mcgill.ca
Tue Nov 21 20:52:14 CET 2006

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)])
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) 


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

other attached packages:


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