R/data.R

In CePa: Centrality-Based Pathway Enrichment

# == title (data:gene.list)
# Differential gene list and background gene list
#
# == details
# Differential gene list and background gene list was extracted from
# microarray data from GEO database. The accession number for the data set
# is GSE22058. The t-test was applied to find differentially expressed genes.
# Top 2000 genes were selected as the gene list.
#
# == value
# A list containing two componets:
#
# -``bk`` background gene list, gene symbol
# -``dif`` differentially expressed gene list, gene symbol
#
# == examples
# data(gene.list)
# names(gene.list)



# == title (data:PID.db)
# pathway catalogues from Pathway Interaction Database(PID)
#
# == details
# The pathway data is parsed from XML format file provided by PID FTP site.
# The perl code for parsing pathway data can be found at author's website
# (http://mcube.nju.edu.cn/jwang/lab/soft/cepa/index.html ).
#
# There are four pathway catalogues which are NCI_Nature, BioCarta, KEGG
# and Reactome.
#
# Each catalogue contains at least three members: pathway list (pathList), 
# interaction list (interactionList) and mappings from node id to gene id (mapping). 
# The pathway list contains a list of pathways in which each pathway is represented
# by a list of interaction id. The interactions can be queried from the interaction list
# by the interaction id. The interaction list data is represented as a data frame
# in which the first column is the interaction id, the second column is the input
# node id and the third column is the output node id. In real biological pathways,
# a node in the pathway can be proteins, complex, families and none-gene nodes, so the 
# mapping from node ids to gene ids is also provided. It must be noted that in this
# package, gene symbol is selected as the primary gene id, so if users apply the PID.db
# data, they should pay attension to the gene ids they transform.
#
# Besides, in each catalogue, there also a node.name, node.type and version data.
# The node.name provides the custumed name for each node. The node.type provides the 
# type for each node (e.g. it is a complex or compound). The version provides the version
# of the catalogue data.
#
# Data has been updated to the lastest version by the day the package released (at 2012_07_19 09:34::20).
#
# Note only part of pathways in the XML file are listed on the PID website. Also, 
# we have set the minimum and maximum connected nodes when extracting pathways 
# from PID, so not all the pathways listed on the PID website are in PID.db.
#
# == value
# A list containing four component:
#
# -NCI NCI_Nature-curated pathway catalogue
# -BioCarta BioCarta pathway catalogue
# -KEGG KEGG pathway catalogue
# -Reactome Reactome pathway catalogue
#
# Each pathway catalogue is a ``pathway.catalogue`` class object. Each pathway
# catalogue can be used directly in `cepa.all` and `cepa`
#
# == examples
# data(PID.db)
# names(PID.db)
# PID.db$NCI
# plot(PID.db$NCI)
#