R version 4.5.0 RC (2025-04-04 r88118 ucrt) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(WayFindR) > ## input directly from file > xmlfile <- system.file("pathways/kegg_hsa00510.xml", package = "WayFindR") > > entries <- collectEntries(xmlfile, "one") > class(entries) [1] "data.frame" > table(entries$Type) compound gene group map ortholog 38 73 3 9 1 > head(entries) GraphId label Type hsa:199857 39 ALG14 gene hsa:54344 40 DPM3 gene hsa:8818 41 DPM2 gene path:hsa00513 42 Various types of N-glycan biosynthesis map G10596 43 (GlcNAc)2 (Man)7 (PP-Dol)1 compound hsa:29929 44 ALG6 gene > > reac <- collectReactions(xmlfile) > dim(reac) [1] 39 3 > table(reac$MIM) # all irreversible irreversible 39 > > rela <- collectRelations(xmlfile) > class(rela) [1] "data.frame" > dim(rela) [1] 57 3 > table(rela$MIM) ECrel ECrel|compound PPrel maplink|compound 4 38 2 13 > > proc.time() user system elapsed 11.75 1.40 23.51