## ---- echo = FALSE------------------------------------------------------------ knitr::opts_chunk$set( eval=FALSE ) ## ----------------------------------------------------------------------------- # if(!"rWikiPathways" %in% installed.packages()){ # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("rWikiPathways") # } # library(rWikiPathways) ## ----------------------------------------------------------------------------- # listOrganisms() ## ----------------------------------------------------------------------------- # hs.pathways <- listPathways('Homo sapiens') # hs.pathways ## ----------------------------------------------------------------------------- # ?listPathways # length(hs.pathways) ## ----------------------------------------------------------------------------- # ?listPathwayIds # ?listPathwayNames # ?listPathwayUrls ## ----------------------------------------------------------------------------- # tnf.pathways <- findPathwaysByXref('TNF','H') # tnf.pathways ## ----------------------------------------------------------------------------- # ?findPathwayIdsByXref # ?findPathwayNamesByXref # ?findPathwayUrlsByXref ## ----------------------------------------------------------------------------- # getPathwayInfo('WP554') ## ----------------------------------------------------------------------------- # getXrefList('WP554','L') ## ----------------------------------------------------------------------------- # getXrefList('WP554', 'En') ## ----------------------------------------------------------------------------- # getXrefList('WP554', 'Ch') # getXrefList('WP554', 'Ce') # getXrefList('WP554', 'Cs') ## ----------------------------------------------------------------------------- # gpml <- getPathway('WP554') ## ----------------------------------------------------------------------------- # downloadPathwayArchive() ## ----------------------------------------------------------------------------- # downloadPathwayArchive(organism="Mus musculus", format="gmt") ## ----------------------------------------------------------------------------- # downloadPathwayArchive(date="20171010", organism="Mus musculus", format="gmt") ## ----------------------------------------------------------------------------- # browseVignettes('rWikiPathways') # help(package='rWikiPathways')