[BioC] from rat codelink to human locuslink

[Weiwei Shi]

Hi, there:

I like the getHomolog solution (since the first one seems not workable
for me) but i need to do some modification since there is an issue
like this
> getHomolog(id=ratUnigene[5], from.type="unigene", to.type="entrezgene",
+ from.mart=rat, to.mart=human)
               V1              V2    V3
1 ENSG00000095397 ENST00000362057 25861
2 ENSG00000095397 ENST00000265134    NA
3 ENSG00000095397 ENST00000361938 25861
4 ENSG00000095397 ENST00000374059    NA
5 ENSG00000095397 ENST00000374057    NA

For one ratUnigene, there are five $V3.
t1 <- sapply(ratUnigene, function(i) unique(getHomolog(id=i,
from.type="unigene", to.type="entrezgene",
from.mart=rat, to.mart=human)$V3)[1])

> as.character(t1)
 [1] "NULL"   "10402"  "NULL"   "NULL"   "25861"  "8706"   "195827"
 [8] "NULL"   "NULL"   "NULL"   "NULL"   "NULL"   "55884"  "NULL"
[15] "NULL"   "3898"   "23324"  "NULL"   "NULL"   "NULL"

Of course, I assume, there are only the same id and NA for $V3.

However, since I have ~7400 unigenes, it is supposed to end after 78
min. However, I run into a connection issue:

> system.time(t1 <- sapply(ratUnigene, function(i) unique(getHomolog(id=i, from.type="unigen
e", to.type="entrezgene",from.mart=rat, to.mart=human)$V3)[1]))
Error in postForm(paste(to.mart at host, "?", sep = ""), query = xmlQuery) :
        couldn't connect to host
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Timing stopped at: 1.641 0.22 444.603 0 0

So, I am wondering if there is a way to download a lookup table and do
it locally. By the way, 78 minutes to do 7400 times' conversions.



Weiwei