1) getGOInfo man page:
   Chemical
     Component Ontology.
 there is no Chemical component - please be more careful

  - it should allow you to drop nodes for specified evidence codes
------This Should be done. I did not use the dropECode since it was not doing what I wanted...I wrote a small function to do this.

2) createGOMatrix - it should take the output of getGOInfo as input,
 otherwise getGOInfo should be hidden from view

  createGOMatrix = function(cMembers = getGOInfo(), wantList=FALSE)

 is probably a better way to do this

 then you could just call createGODF with two arguments (and this want
 list thing could go away?). I think this function should return a matrix.
------Working on this...this should be done.

3) same basic idea for the mips code, best to keep things seperate
-----Working on this...this sould be done now as well.

4) mergeBGMat:
 says:     This function takes the union of the row names of matrix1 and
     matrix2 for the rownames of the aggregate matrix, and concatonates
 
 but the arguments are mat1 and mat2 not matrix1 and matrix2. It is very 
 important that you get this level of detail right.

 Don't say things like: Again this is an...,
  this might be the only manual page they read (so where does "Again" come
  from?). Describe in enough detail for any reader to know what you are 
  doing. No where does it tell me that you are merging these two matrices,
 that some action is being taken to resolve overlaps etc. 
-----I deleted this function...done.

5) I get gene names like:
  [1] "Q0105"       "Q0045"       "Q0250"       "Q0275"       "Q0080"      
 [6] "Q0085"       "Q0130"       "Q0140"       "RNA_TLC1"    "SNRNA_NME1" 
[11] "RNA_RNASE-P"

 which simply don't seem right to me. The Q ones seem to show up, but the
 other three, I don't know about. Maybe Rachel does?
-----I will talk to Rachel about this.

6) getAPMSData - the man page does not tell us what the options are, so 
 how could we know? Please document. This is also a place to use
 match.arg.
  You seem to process the data from apComplex so explain what is coming
 back and please don't use acronyms (BG Incidence Matrix ?? what is BG
 and surely it is an adjacency matrix if it is anything??)


7) the merging is not doing what I think that it should.
 First, you should use the merge function, for what this is doing, and
 second, I don't see any value in doing it.

 This is the point where we should try to identify which of the 
 putative protein complexes are identical (nearly identical) and
 which are strict subsets of others. That might be one set of calculations,
 that returns those statistics, without performing any merging.
 Then, given those the user might want to set some parameters to 
 do the merging. I think we might want to factor this into two pieces,
 one that computes the statistics and one that merges.

 As we just discussed, the tools for computing some of these quantities
 should be moved here from simulateAPMS, as they more properly seem to 
 fit here (and then simulateAPMS could depend on this package, rather than
 the other way around, which does seem a bit backwards).
 -----This should be done. I will need to create new man files since I have changed the functions to do more things here...will do tonight.


***I have made all the changes to the code itself...I need to update the man pages..will work on that.