funnell / reactomefi Goto Github PK

Using the R cytoscape plugin

HI,
I get error with I set use linkers = TRUE for all version. Any suggestion? Thanks Karim

network <- ReactomeFINetwork("2013", GeneList, use.linkers=TRUE )
Opening and ending tag mismatch: HR line 34 and body
Opening and ending tag mismatch: HR line 1 and html
Premature end of data in tag body line 1
Premature end of data in tag html line 1
Error: 1: Opening and ending tag mismatch: HR line 34 and body
2: Opening and ending tag mismatch: HR line 1 and html
3: Premature end of data in tag body line 1
4: Premature end of data in tag html line 1

Error in [.data.frame(dat, , i) : undefined columns selected
Calls: gene.set.enrichment ... queryAnnotateModules -> df2tsv -> [ -> [.data.frame

need to add tests for cases that return no results at different steps

Right now if the API returns no network an error occurs in the ReactomeFINetwork constructor

Somehow allow creating ReactomeFINetwork objects by providing interaction data rather than computing using the API. These networks can then use the clustering and gene set enrichment analysis.