[BioC] A question about org.Hs.egMAPCOUNTS

[Marc Carlson]

Hi Gilbert,

To answer questions like this you might want to look at the manual page
for count.mappedRkeys() and count.mappedLkeys().  These can be used to
count the number of mapped keys in a mapping.


# An example to give you an idea:
count.mappedRkeys(org.Hs.egGO2EG)

# This gives us:
[1] 8245

# That is the same number as you saw in the MAPCOUNTS, But what exactly
did we just count?
# Lets look at one key just to see:

mappedRkeys(org.Hs.egGO2EG[1])


# So you can see that we were just found that 8245 GO terms are matched
onto some gene!

[1] "GO:0000002"


# So how can we see how many genes are matched onto GO terms??

count.mappedLkeys(org.Hs.egGO2EG)

# which comed out to be 17673
[1] 17673


# And just to verify that the Lkeys are entrez gene IDs:

mappedLkeys(org.Hs.egGO2EG[1])


You may have noticed that the Lkeys are still the entrez gene IDs in
both the "reversed" maps as well as the "forward" maps.  This is because
we are using "undirected" methods as described in the manual page.  So
when using such methods you should pay attention to what you are
counting as this can seem confusing when used with a "reversed" such as
a "GO2EG" mapping.  You might expect that the Lkeys and Rkeys would
switch places, but for these methods they have not.


Hope this clarifies things a bit,


  Marc









On 03/02/2010 01:19 PM, Gilbert Feng wrote:
> Hello, BioC forks,
>
> I notice that org.Hs.egMAPCOUNTS reports that org.Hs.egGO2EG is 8245. Are
> these 8245 genes are unique or, do all of GO terms contain 8245 human genes
> (could be counted many times)? Actually, I wonder how many unique human
> genes in GO and its subdirectories, BP, MF and CC. Is there any function to
> retrieve such information easily or I have to write several lines to do
> that?
>
> Thanks a lot!
>
> Gilbert
>
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