README.md

In ddkale/MetabomapR: R package for MetaboMapR

Metabolomic network edge list generation

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)

##   id   KEGG    CID                            name
## 1 N1 C15973     [] Enzyme N6-(dihydrolipoyl)lysine
## 2 N2 C00026     51                  2-Oxoglutarate
## 3 N3 C05381 440649  3-Carboxy-1-hydroxypropyl-ThPP
## 4 N4 C15972     []        Enzyme N6-(lipoyl)lysine
## 5 N5 C00091 439161                    Succinyl-CoA
## 6 N6 C00042   1110                       Succinate

Convert PubChem CID to tanimoto based chemical similarity

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

##    source target             value
## 16     51 440649 0.158469945355191
## 31     51 439161 0.171122994652406
## 32 440649 439161 0.646788990825688
## 46     51   1110 0.702702702702703
## 47 440649   1110 0.146892655367232
## 48 439161   1110 0.147540983606557

get KEGG based biochemical connections

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

##   source target
## 1 C15972 C15973
## 2 C15973 C16254
## 3 C15973 C16255
## 4 C00026 C00091
## 5 C00026 C00311
## 6 C00026 C05381

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)

##   source target value type
## 1     N4     N1     1 KEGG
## 2     N1    N16     1 KEGG
## 3     N1    N18     1 KEGG
## 4     N2     N5     1 KEGG
## 5     N2     N8     1 KEGG
## 6     N2     N3     1 KEGG

About

• contact: [e-mail]
• updated: 2017-01-07

ddkale/MetabomapR documentation built on May 5, 2019, 7:57 p.m.