Nothing
###
###
###
###
###
###
#-----
#Notes:
#
# MAPCOUNTS : list of numbers of mapped keys per table
#
#-----
###
### org.<species>.eg database
###
###
###
#
# Available org.SPEC.eg.db databases in BioconductoR at end of June 2012 :
# (excerpt of http://www.bioconductor.org/packages/release/BiocViews.html#___AnnotationData )
#
# Package: Maintainer: Title:
# org.Ag.eg.db Biocore Data Team Genome wide annotation for Anopheles
# org.At.tair.db Biocore Data Team Genome wide annotation for Arabidopsis
# org.Bt.eg.db Biocore Data Team Genome wide annotation for Bovine
# org.Ce.eg.db Biocore Data Team Genome wide annotation for Worm
# org.Cf.eg.db Biocore Data Team Genome wide annotation for Canine
# org.Dm.eg.db Biocore Data Team Genome wide annotation for Fly
# org.Dr.eg.db Biocore Data Team Genome wide annotation for Zebrafish
# org.EcK12.eg.db Biocore Data Team Genome wide annotation for E coli strain K12
# org.EcSakai.eg.db Biocore Data Team Genome wide annotation for E coli strain Sakai
# org.Gg.eg.db Biocore Data Team Genome wide annotation for Chicken
# org.Hs.eg.db Biocore Data Team Genome wide annotation for Human
# org.Hs.ipi.db Hong Li A data package containing annotation data for org.Hs.ipi.db
# org.Mm.eg.db Biocore Data Team Genome wide annotation for Mouse
# org.Mmu.eg.db Biocore Data Team Genome wide annotation for Rhesus
# org.Pf.plasmo.db Biocore Data Team Genome wide annotation for Malaria
# org.Pt.eg.db Biocore Data Team Genome wide annotation for Chimp
# org.Rn.eg.db Biocore Data Team Genome wide annotation for Rat
# org.Sc.sgd.db Biocore Data Team Genome wide annotation for Yeast
# org.Sco.eg.db Roxane Legaie Genome wide annotation for Streptomyces coelicolor
# org.Ss.eg.db Biocore Data Team Genome wide annotation for Pig
# org.Tgondii.eg.db Olivier Lucas Genome wide annotation for Toxoplasma gondii
# org.Xl.eg.db Biocore Data Team Genome wide annotation for Xenopus
#
#
# Get <organism> for the org.<organism>.eg.eb-style database names, given one of the
# commonly used and plausible names for the wanted organism (see list above)
#
whop.eg.abbrevForOrganism <- function( organismname )
{
organismname <- gsub( "\\W|_","", organismname )
org <- NULL
try( org <- .WHOPGENenv$eg[["organisms_list"]][[ tolower(organismname) ]] , silent=T)
if( is.null( org ) )
{
cat( paste("Unrecognised organism:",organismname,"\n") )
}
return( org )
}
#
# Is org.<organism>.eg.db loaded ?
#
whop.eg.orgdb_loaded <- function( organismname )
{
paste(sep="","package:org.",whop.eg.abbrevForOrganism( organismname ),".eg.db") %in% search()
}
#
#
#
whop.eg.installdb <- function( organismname )
{
orglibnam <- NULL ; rm(orglibnam)
biocLite <- NULL ; rm(biocLite)
abbrev <- whop.eg.abbrevForOrganism( organismname )
if( ! is.null( abbrev ) )
{
source("http://bioconductor.org/biocLite.R")
orglibnam <- paste(sep="","org.",abbrev,".eg.db" )
biocLite( orglibnam )
if( library( orglibnam, character.only=TRUE ) ) return(TRUE)
print( .WHOPGENenv$pp("Could not load library '",orglibnam,"'!") )
}
#
return(FALSE)
}
##########
#
# Load an org.<organism>.eg.db and, if needed, install it first from BioconductoR
#
##########
whop.eg.load_orgdb <- function( organismname, install.if.missing=F )
{
# find abbrev used in the bioconductor package names
orgdblibnam <- NULL
abbrev <- whop.eg.abbrevForOrganism( organismname )
# if the abbreviation was found,...
if( ! is.null( abbrev ) )
{
# try to load the database
if( ! whop.eg.orgdb_loaded( abbrev ) )
{
orgdblibnam <- paste(sep="","org.",abbrev,".eg.db" )
print( .WHOPGENenv$pp("Loading ", orgdblibnam,"...") )
if( ! library( orgdblibnam, character.only=TRUE ) )
{
if( ! install.if.missing )
{
print( .WHOPGENenv$pp("Could not load library '",orgdblibnam,"'!") )
return( FALSE )
}
return( whop.eg.installdb( organismname ) )
}#..if( could not load org.eg.db package )
}#...if( org.eg.db for organism not loaded )
return( TRUE )
}#...if ( could translate organismname to abbreviation )
#
return( FALSE );
}
##########
#
# Select an organism
#
##########
whop.eg.selectOrganism <- function( organismname, dontload=FALSE, install.if.missing=F )
{
# find abbrev used in the bioconductor package names
abbrev <- whop.eg.abbrevForOrganism( organismname )
# if the abbreviation was found,...
if( ! is.null( abbrev ) )
{
# set the organism abbreviation currently used
.WHOPGENenv$eg[["organism_name"]] <- abbrev
res = TRUE
# also try to load the database
if( (!dontload) && (! whop.eg.orgdb_loaded( abbrev )) )
{
res = whop.eg.load_orgdb( abbrev , install.if.missing )
}
return( res )
}
return(FALSE)
}
##########
#
# Given a common gene alias (like LCT, MTLA1) into the numeric identifier used in eg
#
##########
#
#
whop.eg.eg_lookupAll <- function( id, subdbname, db=.WHOPGENenv$eg[["databasename"]] ) mget( id , get( paste(sep="","org.",.WHOPGENenv$eg[["organism_name"]],".eg",subdbname) ) )
# map a single Entrez gene id to some information in a given table
#
whop.eg.eg_lookupSingle <- function( id, subdbname, db=.WHOPGENenv$eg[["databasename"]] ) mget( id , get( paste(sep="","org.",.WHOPGENenv$eg[["organism_name"]],".eg",subdbname) ) )[[1]]
# map each of a vector of Entrez gene ids to some information in a given table
#
whop.eg.eg_lookup <- function( ids, subdbname, db=.WHOPGENenv$eg[["databasename"]] )
{
res<-c();
x <- 0
for( x in ids )
{
res <- c( res, mget( x , get( paste(sep="","org.",.WHOPGENenv$eg[["organism_name"]],".eg",subdbname) ) ) )
}
return (res);
}
# map each of a vector of Entrez gene ids to some information in a given table
#
whop.eg.eg_RevLookup <- function( ids, subdbname, db=.WHOPGENenv$eg[["databasename"]] )
{
res<-c();
y <- 0
for( y in ids )
{
res <- c( res, mget( y ,
AnnotationDbi::revmap(
get( paste(sep="","org.",.WHOPGENenv$eg[["organism_name"]],".eg",subdbname) )
)
)
)
}
return (res);
}
#################################################################
#
# Other Identifiers -> EG
#
#################################################################
# From
#
whop.eg.fromAlias <- function( id , db=.WHOPGENenv$eg[["databasename"]] ) whop.eg.eg_lookup( id, "ALIAS2EG", db )
whop.eg.fromAccnum <- function( id , db=.WHOPGENenv$eg[["databasename"]] ) whop.eg.eg_lookup( id, "ACCNUM2EG", db )
whop.eg.fromEnsembl <- function( id , db=.WHOPGENenv$eg[["databasename"]] ) whop.eg.eg_lookup( id, "ENSEMBL2EG", db )
whop.eg.fromEnsemblProt <- function( id , db=.WHOPGENenv$eg[["databasename"]] ) whop.eg.eg_lookup( id, "ENSEMBLPROT2EG", db )
whop.eg.fromEnsemblTrans <- function( id , db=.WHOPGENenv$eg[["databasename"]] ) whop.eg.eg_lookup( id, "ENSEMBLTRANS2EG", db )
whop.eg.fromEnzyme <- function( id , db=.WHOPGENenv$eg[["databasename"]] ) whop.eg.eg_lookup( id, "ENZYME2EG", db )
whop.eg.toEnzyme <- function( id , db=.WHOPGENenv$eg[["databasename"]] ) whop.eg.eg_lookup( id, "ENZYME", db )
whop.eg.fromGO <- function( id , db=.WHOPGENenv$eg[["databasename"]] ) whop.eg.eg_lookup( id, "GO2EG", db )
whop.eg.fromGO2AllEgs <- function( id , db=.WHOPGENenv$eg[["databasename"]] ) whop.eg.eg_lookup( id, "GO2ALLEGS", db )
whop.eg.fromOmim <- function( id , db=.WHOPGENenv$eg[["databasename"]] ) whop.eg.eg_lookup( id, "OMIM2EG", db )
whop.eg.fromPath <- function( id , db=.WHOPGENenv$eg[["databasename"]] ) whop.eg.eg_lookup( id, "PATH2EG", db )
whop.eg.fromPmid <- function( id , db=.WHOPGENenv$eg[["databasename"]] ) whop.eg.eg_lookup( id, "PMID2EG", db )
whop.eg.fromRefseq <- function( id , db=.WHOPGENenv$eg[["databasename"]] ) whop.eg.eg_lookup( id, "REFSEQ2EG", db )
whop.eg.fromUnigene <- function( id , db=.WHOPGENenv$eg[["databasename"]] ) whop.eg.eg_lookup( id, "UNIGENE2EG", db )
whop.eg.fromUniprot <- function( id , db=.WHOPGENenv$eg[["databasename"]] ) whop.eg.eg_lookup( id, "UNIPROT2EG", db )
# To
#
whop.eg.toAlias <- function( id , db=.WHOPGENenv$eg[["databasename"]] ) whop.eg.eg_RevLookup( id, "SYMBOL2EG", db )
whop.eg.toAccnum <- function( id , db=.WHOPGENenv$eg[["databasename"]] ) whop.eg.eg_RevLookup( id, "ACCNUM2EG", db )
whop.eg.toEnsembl <- function( id , db=.WHOPGENenv$eg[["databasename"]] ) whop.eg.eg_RevLookup( id, "ENSEMBL2EG", db )
whop.eg.toEnsemblProt <- function( id , db=.WHOPGENenv$eg[["databasename"]] ) whop.eg.eg_RevLookup( id, "ENSEMBLPROT2EG", db )
whop.eg.toEnsemblTrans <- function( id , db=.WHOPGENenv$eg[["databasename"]] ) whop.eg.eg_RevLookup( id, "ENSEMBLTRANS2EG", db )
#whop.eg.toEnzyme <- function( id , db=.WHOPGENenv$eg[["databasename"]] ) whop.eg.eg_RevLookup( id, "ENZYME2EG", db )
whop.eg.toGO <- function( id , db=.WHOPGENenv$eg[["databasename"]] ) whop.eg.eg_RevLookup( id, "GO2EG", db )
#whop.eg.fromGO2AllEgs <- function( id , db=.WHOPGENenv$eg[["databasename"]] ) whop.eg.eg_lookup( id, "GO2ALLEGS", db )
whop.eg.toOmim <- function( id , db=.WHOPGENenv$eg[["databasename"]] ) whop.eg.eg_RevLookup( id, "OMIM2EG", db )
whop.eg.toPath <- function( id , db=.WHOPGENenv$eg[["databasename"]] ) whop.eg.eg_RevLookup( id, "PATH2EG", db )
whop.eg.toPmid <- function( id , db=.WHOPGENenv$eg[["databasename"]] ) whop.eg.eg_RevLookup( id, "PMID2EG", db )
whop.eg.toRefseq <- function( id , db=.WHOPGENenv$eg[["databasename"]] ) whop.eg.eg_RevLookup( id, "REFSEQ2EG", db )
whop.eg.toUnigene <- function( id , db=.WHOPGENenv$eg[["databasename"]] ) whop.eg.eg_RevLookup( id, "UNIGENE2EG", db )
whop.eg.toUniprot <- function( id , db=.WHOPGENenv$eg[["databasename"]] ) whop.eg.eg_RevLookup( id, "UNIPROT2EG", db )
#PFAM?
# > org.Hs.egPFAM$`1`
# IPI00022895 IPI00644018 IPI00902880
# NA NA NA
# > names(org.Hs.egPFAM$`1`)
# [1] "IPI00022895" "IPI00644018" "IPI00902880"
#
#PROSITE?
#
# same pattern as with PFAM
#
#################################################################
#
# EG -> Other Identifiers
#
#################################################################
#org.Hs.egACCNUM org.Hs.egENSEMBLTRANS org.Hs.egMAP org.Hs.egPFAM org.Hs.egUCSCKG
#org.Hs.egACCNUM2EG org.Hs.eg_dbfile org.Hs.egENSEMBLTRANS2EG org.Hs.egMAP2EG org.Hs.egPMID org.Hs.egUNIGENE
#org.Hs.egALIAS2EG org.Hs.eg_dbInfo org.Hs.egENZYME org.Hs.egMAPCOUNTS org.Hs.egPMID2EG org.Hs.egUNIGENE2EG
#org.Hs.egCHR org.Hs.eg_dbschema org.Hs.egENZYME2EG org.Hs.egOMIM org.Hs.egPROSITE org.Hs.egUNIPROT
#org.Hs.egCHRLENGTHS org.Hs.egENSEMBL org.Hs.egGENENAME org.Hs.egOMIM2EG org.Hs.egREFSEQ org.Hs.eg.db::
#org.Hs.egCHRLOC org.Hs.egENSEMBL2EG org.Hs.egGO org.Hs.egORGANISM org.Hs.egREFSEQ2EG
#org.Hs.egCHRLOCEND org.Hs.egENSEMBLPROT org.Hs.egGO2ALLEGS org.Hs.egPATH org.Hs.egSYMBOL
whop.eg.toAccnum <- function( id , db=.WHOPGENenv$eg[["databasename"]] ) whop.eg.eg_lookup( as.character(id) ,"ACCNUM",db)
#################################################################
#
# Other handy lookup functions
#
#################################################################
##########
# gene descriptive name for egID
#
whop.eg.genename <- function( id, db=.WHOPGENenv$eg[["databasename"]] ) whop.eg.eg_lookup( id, "GENENAME", db )
##########
# enzyme nomenclature identifiers for egID
#
whop.eg.enzyme <- function( id, db=.WHOPGENenv$eg[["databasename"]] ) whop.eg.eg_lookup( id, "ENZYME", db )
##########
# chromosomal region for egID
#
whop.eg.region <- function( id, db=.WHOPGENenv$eg[["databasename"]] ) c( whop.eg.eg_lookup( id, "CHRLOC", db ), whop.eg.eg_lookup( id, "CHRLOCEND", db ) )
##########
# chromosome on which gene entrez <id> lies
#
whop.eg.chromosome <- function( id, db=.WHOPGENenv$eg[["databasename"]] ) whop.eg.eg_lookup( id, "CHR", db )
##########
# GO identifiers relating to gene with entrez <id>
#
whop.eg.goIds <- function( id, db=.WHOPGENenv$eg[["databasename"]] ) whop.eg.eg_lookup( id, "GO", db )
#MAP2EG (cytogenetic location) e.g. 19q13.4
#################################################################
#
# Miscelleaneous functions
#
#################################################################
whop.eg.Organism <- function() get( paste(sep="","org.",.WHOPGENenv$eg[["organism_name"]],".egORGANISM") )
#################################################################
#
# KEGG related (pathways)
#
#################################################################
whop.eg.keggpathways <- function( id, db=.WHOPGENenv$eg[["databasename"]] ) whop.eg.eg_lookup( id, "PATH", db )
# print URL pointing to the KEGG pathway webpage for a given KEGG pathway ID
#
#NOTE: tested to work correctly with a vector of pathwayids
whop.kegg.pathway_url <- function( pathwayids ) print( .WHOPGENenv$pp( "http://www.genome.jp/dbget-bin/www_bget?pathway+",.WHOPGENenv$eg[["organism_prefixed"]][ tolower(.WHOPGENenv$eg[["organism_name"]]) ],pathwayids) )
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