[BioC] pathway ID in KEGG.db

[Marc Carlson]

Hi Ed,

The confusion is because you have an "apples to oranges" comparison 
here.  There are 390 unique KEGG IDs in the DB.  That means that there 
are only 390 KEGG names for those pathways.  However, those pathway IDs 
are matched up to over 3000 different external gene IDs which is why the 
second mapping is so much larger.  You can learn more about the 
different mappings by reading their manual pages like this:

help("KEGGPATHID2NAME")

help("KEGGPATHID2EXTID")


   Marc


 >


On 07/05/2012 12:48 AM, Ed wrote:
> Hi there,
>
> I found the number of pathways in KEGGPATHID2NAME is 390 while that
> in KEGGPATHID2EXTID is 3152. Am I missing something? BTW, the pathway id's
> used in this package seems inconsistent too.
>
> Thanks.
>
> Ed
>
>> ?KEGGPATHID2NAME
>>               xx<- as.list(KEGGPATHID2NAME)
>>               if(length(xx)>  0){
> +                      # get the value for the first key
> +                      xx[[1]]
> +                      # Get the values for a few keys
> +                      if(length(xx)>= 3){
> +                              xx[1:3]
> +                      }
> +              }
> $`00010`
> [1] "Glycolysis / Gluconeogenesis"
>
> $`00020`
> [1] "Citrate cycle (TCA cycle)"
>
> $`00030`
> [1] "Pentose phosphate pathway"
>
>> length(xx)
> [1] 390
>
>
> ?KEGGPATHID2EXTID
>               xx<- as.list(KEGGPATHID2EXTID)
>               if(length(xx)>  0){
>                       # Get the value of the first key
>                       xx[[1]]
>                       # Get the values for multiget for a few keys
>                       if(length(xx)>= 3){
>                               xx[1:3]
>                       }
>               }
>> length(xx)
> [1] 3152
>
>> sessionInfo()
> R version 2.14.1 (2011-12-22)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936
> [2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936
> [3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936
> [4] LC_NUMERIC=C
> [5] LC_TIME=Chinese (Simplified)_People's Republic of China.936
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] KEGG.db_2.6.1         RSQLite_0.11.1        DBI_0.2-5
> [4] AnnotationDbi_1.16.18 Biobase_2.14.0
>
> loaded via a namespace (and not attached):
> [1] IRanges_1.12.5 tools_2.14.1
>
> 	[[alternative HTML version deleted]]
>
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