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bobthecat/ppi.r

Created June 4, 2012 03:47
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ppi
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ppi.r
ppi <- get.ppiNCBI(head(glist, 20))
[1] "7 interactions found"
## Annotate the gene list with Mus musculus metadata
library(org.Mm.eg.db)
ppi$egSymbol <- mget(ppi$egID, envir=org.Mm.egSYMBOL, ifnotfound=NA)
ppi$intID <- mget(ppi$intSymbol, envir=org.Mm.egSYMBOL2EG, ifnotfound=NA)
ppi <- ppi[,c(3,2,1,4)]
ppi
egSymbol intSymbol egID intID
1 Ifi202b Pou5f1 26388 18999
2 Hes5 Jak2 15208 16452
3 Eya1 Polr2a 14048 20020
4 Eya1 Rbck1 14048 24105
5 Eya1 Sharpin 14048 106025
6 Cdk6 TGFBR1 12571 NA
7 Bcl11a Sirt1 14025 93759
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