[Bioc-devel] new package: annotate function interaction from Reactome DB

[Karim Mezhoud]

Dear bioC devel,
I write an annotate package named reactomeFI to avoid the big size files in
/extdata folder.
Finally when compressed the txt file to RDS format I reduce enough the size
of files.

reactomeFI provides annotation that do not exist in any other package (to
my knowledge).
Nor reactome.db nor PSICQUIC provide the arrow direction and the type of
interaction.

library(reactomeFI)
dim(ld_reactomeFI(2014))
[1] 217249      5
> dim(ld_reactomeFI(2015))
[1] 229300      5
> head(ld_reactomeFI(version= 2015))
                  Gene1  Gene2        Annotation Direction Score
1                16-5-5  CDC42         predicted         -  0.82
2                16-5-5   RHOJ         predicted         -  0.82
3                16-5-5   RHOQ         predicted         -  0.82
4 <DELTA>FAS/APO-1/CD95    BID          activate        ->  1.00
5 <DELTA>FAS/APO-1/CD95 CASP10           complex         -  1.00
6 <DELTA>FAS/APO-1/CD95   DAXX complex; reaction         -  1.00

> tail(ld_reactomeFI(2015))
        Gene1  Gene2     Annotation Direction Score
229295    ZP3    ZP4        complex         -  1.00
229296   ZPR1    ZYX      predicted         -  0.59
229297   ZW10 ZWILCH complex; input         -  1.00
229298   ZW10  ZWINT complex; input         -  1.00
229299 ZWILCH  ZWINT complex; input         -  1.00
229300   ZXDA   ZXDC      predicted         -  0.59

I can add other argument to specify the type of interaction or direction as

ld_reactomeFI(version=2014, type=c(activated, complex),
direction="arrowhead")

I am ready to submit this package if you consider as new annotate
information.
Thank you,
Karim

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