# OmnipathR
utility functions to work with Omnipath in R
## Description
basic utility functions to download and interact with data from Omnipath webservice (www.omnipathdb.org).
## Install
you can use the `devtools` package to install from the GitHub in one line:
```{r}
if(!require(devtools)) install.packages("devtools")
devtools::install_github("saezlab/omnipathR")
```
Or download, unzip and install the usual way:
`install.packages('./OmnipathR',repo=NULL)`
## Examples
Download post-translational modifications:
`ptms = import_Omnipath_PTMS(filter_databases=c("PhosphoSite", "Signor"))`
Download protein-protein interactions:
`interactions = import_Omnipath_Interactions(filter_databases=c("SignaLink3","PhosphoSite", "Signor"))`
Convert to igraph objects:
`ptms_g = ptms_graph(ptms = ptms )`
`OPI_g = interaction_graph(interactions = interactions )`
Print some interactions:
```{r}
print_interactions(head(ptms))
enzyme interaction substrate modification nsources nrefs
1 PRKCA (P17252) ==( + )==> NPHS1_T1120 (O60500) phosphorylation 3 0
2 PRKCA (P17252) ==( + )==> NPHS1_T1125 (O60500) phosphorylation 3 0
3 PRKCA (P17252) ==( + )==> PDE3A_S465 (Q14432) phosphorylation 3 0
4 PRKCA (P17252) ==( + )==> PDE3A_S428 (Q14432) phosphorylation 3 0
5 PRKCA (P17252) ==( + )==> PDE3A_S438 (Q14432) phosphorylation 3 0
6 PRKCA (P17252) ==( + )==> PDE3A_S312 (Q14432) phosphorylation 3 0
```
Interactions with references:
`print_interactions(tail(ptms),writeRefs=T)`
Find interactions between kinase and substrate:
```{r}
print_interactions(dplyr::filter(ptms,enzyme_genesymbol=="MAP2K1",substrate_genesymbol=="MAPK3"))
enzyme interaction substrate modification nsources nrefs
2 MAP2K1 (Q02750) ==( + )==> MAPK3_Y204 (P27361) phosphorylation 6 13
1 MAP2K1 (Q02750) ==( + )==> MAPK3_T202 (P27361) phosphorylation 6 8
3 MAP2K1 (Q02750) ==( + )==> MAPK3_T80 (P27361) phosphorylation 1 0
4 MAP2K1 (Q02750) ==( + )==> MAPK3_Y222 (P27361) phosphorylation 1 0
5 MAP2K1 (Q02750) ==( + )==> MAPK3_Y210 (P27361) phosphorylation 1 0
6 MAP2K1 (Q02750) ==( + )==> MAPK3_T207 (P27361) phosphorylation 1 0
```
Find shortest paths on the directed network between proteins:
```{r}
> printPath_es(shortest_paths(OPI_g,from = "TYRO3",to = "STAT3", output = 'epath')$epath[[1]],OPI_g)
source interaction target nsources nrefs
1 TYRO3 (Q06418) ==( + )==> PIK3R1 (P27986) 4 3
2 PIK3R1 (P27986) ==( ? )==> AR (P10275) 3 3
3 AR (P10275) ==( ? )==> STAT3 (P40763) 3 4`
```
Find all shortest paths between proteins:
```{r}
printPath_vs(all_shortest_paths(OPI_g,from = "DYRK2",to = "MAPKAPK2")$res,OPI_g)
[1] "pathway 1: DYRK2 -> TP53 -> MAPK3 -> MAPKAPK2"
source interaction target nsources nrefs
1 DYRK2 (Q92630) ==( + )==> TP53 (P04637) 6 102
2 TP53 (P04637) ==( ? )==> MAPK3 (P27361) 4 6
3 MAPK3 (P27361) ==( + )==> MAPKAPK2 (P49137) 3 4
[1] "pathway 2: DYRK2 -> TP53 -> MAPK14 -> MAPKAPK2"
source interaction target nsources nrefs
1 DYRK2 (Q92630) ==( + )==> TP53 (P04637) 6 102
2 TP53 (P04637) ==( ? )==> MAPK14 (Q16539) 3 8
3 MAPK14 (Q16539) ==( + )==> MAPKAPK2 (P49137) 19 40
[1] "pathway 3: DYRK2 -> TP53 -> MAPK1 -> MAPKAPK2"
source interaction target nsources nrefs
1 DYRK2 (Q92630) ==( + )==> TP53 (P04637) 6 102
2 TP53 (P04637) ==( ? )==> MAPK1 (P28482) 5 11
3 MAPK1 (P28482) ==( + )==> MAPKAPK2 (P49137) 9 11
```
## Feedbacks, bug reports, features
Feedbacks and bugreports are always very welcomed!
Please use the Github issue page to report bugs or for questions: https://github.com/saezlab/OmnipathR/issues.
Many thanks!
