ReactomeFINetwork with use.linkers = TRUE about reactomefi HOT 6 CLOSED

Hi Karim,

Sorry about this. Unfortunately it seems linkers=TRUE is broken. The package connects to the ReactomeFI plugin's web service, and it turns out that the linkers=TRUE functionality doesn't work on the web service. The Cytoscape plugin still works, because this functionality has been re-implemented in the plugin code itself!
I'll need to have a look at how the plugin code implements linker gene functionality.

from reactomefi.

Hi Tyler,
I am not familiar with Java and eclipse to look also on it.
I am interested to learn how reactomefi connects to the ReactomeFI web service. In which file can I find the connection code?
is the access to web service is public/free?
Thanks

from reactomefi.

This file https://github.com/funnell/reactomefi/blob/master/R/ReactomeFIService.R has functions that wraps some of the web service. Access to the web service is free and I suppose it's public, but not really documented, last I checked. I wrote the above file by looking at the plugin Java code, and by asking the plugin author for help, when needed.

from reactomefi.

HI,
use.linker =TRUE is fixed.

getReactomeFI(2014, GeneList)
first.protein second.protein
1 IFI16 TP53
2 PML TP53
3 BRCA1 TP53
4 BRCA1 IFI16
5 BRCA1 NBN
getReactomeFI(2014, GeneList, use.linkers = TRUE)
first.protein second.protein
1 UBB BRCA1
2 EGR1 DKK3
3 TP53 BRCA1
4 PML TP53
5 TP53 UBB
6 NBN BRCA1
7 TP53 IFI16
8 MYO6 UBB
9 EGR1 TP53
10 EGR1 BRCA1
11 IFI16 BRCA1
12 EGR1 UBB

from reactomefi.

This is encouraging! Did you just change the version year? Was this the same set of genes you first noticed the error with?

from reactomefi.

All versions work. Not the same set of genes But I tried many genes. Bad symbol may cause error message.
Guanming Wu was fixed the error on the server.

from reactomefi.