[Rd] Pb with agrep()

[Herve Pages]

Happy new year everybody,


I'm getting the following while trying to use the agrep() function:

 > pattern <- "XXX"
 > subject <- c("oooooo", "oooXooo", "oooXXooo", "oooXXXooo")
 > max <- list(ins=0, del=0, sub=0) # I want exact matches only
 > agrep(pattern, subject, max=max)
[1] 4

OK

 > max$sub <- 1 # One allowed substitution
 > agrep(pattern, subject, max=max)
[1] 3 4

OK

 > max$sub <- 2 # Two allowed substitutions
 > agrep(pattern, subject, max=max)
[1] 3 4

Wrong!

 > sessionInfo()
R version 2.3.0, 2005-12-22, x86_64-unknown-linux-gnu
 
attached base packages:
[1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets"
[7] "base"
 
other attached packages:
Biostrings
   "1.5.6"

Cheers,


Hervé


-- 
------------------------
Hervé Pagès
E-mail: hpages at fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319