In dgrapov/metabomapr: R package for MetaboMapR

Metabolomic network edge list generation

Install

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ChemmineR")

devtools::install_github('dgrapov/metabomapr')

Supported connections:

structural similarity based on pubChem CID
biochemical connections based on KEGG

See MetaMapR for more features.

Examples

#devtools::install_github("dgrapov/metabomapr")
library(metabomapr)
library(dplyr)

Demo data

main<-test_data() 
head(main)

Convert PubChem CID to tanimoto based chemical similarity

type<-'CID'
id<-main[,type]
cid_el<-CID_tanimoto(id,as='edge.list')
head(cid_el)

get KEGG based biochemical connections

type<-'KEGG'
id<-main[,type]
kegg_el<-get_KEGG_edgeList(id)
head(kegg_el)

Combine edge lists using a common index

type<-'CID'
cid_el<- cid_el %>%
  convert_edgeIndex(.,start=type,end='id',db=main) %>%
  data.frame(.,cid_el %>% select(-source,-target),type=type)

type<-'KEGG'
kegg_el<- kegg_el %>%
  convert_edgeIndex(.,start=type,end='id',db=main) %>%
  data.frame(.,kegg_el %>% select(-source,-target),value=1,type=type)

#combined edge list
el<-rbind(kegg_el,cid_el)
head(el)

Using opencpu API

Define server

options('open_cpu_url' = 'http://localhost/ocpu/')
options('metabomapr_url' = 'library/metabomapr/R/' )

Make call using simple opencpuclient

library(ocpuclient)
type<-'CID'
id<-main[,type]

body<-list(type=type,cids=id,as='edge.list')

fun<-'CID_tanimoto'

x<-ocpuclient:::ocpu_post(fun,body=body,pkg_url = getOption('metabomapr_url'), base_url=getOption('open_cpu_url'))

x$results