[BioC] organism = mouse or Mus Musculus in AnnBuilder

[Christopher Wilkinson]

I have a query about the format of the organism name to use in ABPkgBuilder and
getSrcUrl functions of AnnBuilder. It seems in some functions organism should be
the official name (eg Mus Musculus) but in other functions it should be the
common name (eg mouse).

The vignette states that you can get the src URls by calling

mySrcUrl <- getSrcUrl("all","mouse")
However this fails for Golden Path (UCSC) Url. The fix is to use the scientific
name Mus Musculus. e.g.
mySrcUrl <- getSrcUrl("all","Mus Musculus")

When calling the ABPkgBuilder function it states that the organism argument may
only be "human", "mouse" or "rat".

I assume if I use Mus Musculus in getSrcUrl and mouse in ABPkgBuilder all will
be ok. This seems a little inconsistent so are there plans to accept either
common or official name? I assume if I use organism = "Mus Musculus" in
ABPkgBuilder it will generate an error.

Cheers
Chris

(RH9 Linux, R 2.1.0, BioC 1.6 = AnnBuilder 1.5.31)

Dr Chris Wilkinson

Senior Research Officer (Bioinformatics) | ARC Research Associate
Child Health Research Institute (CHRI)   | Microarray Analysis Group
7th floor, Clarence Rieger Building      | Room 121
Women's and Children's Hospital          | School of Applied Mathematics
72 King William Rd, North Adelaide, 5006 | The University of Adelaide, 5005

Math's Office (Room 121)        Ph: 8303 3714
CHRI   Office (CR2 52A)         Ph: 8161 6363

Christopher.Wilkinson at adelaide.edu.au

http://mag.maths.adelaide.edu.au/crwilkinson.html