inst/doc/Overview.R

In rWikiPathways: rWikiPathways - R client library for the WikiPathways API

## ---- 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)

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#      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')