Annotation package that collates several annotation resources.

Description

This data object was automatically created by Bioconductor Core Team. It represents a collection of annotation packages that can be used as a single object named Homo.sapiens. This object can be used with the standard four accessor method for all AnnotationDbi objects. Namely: cols, keytype, keys and select. Users are encouraged to read the vignette from the OrganismDbi package for more details.

Usage

library(Homo.sapiens)

Examples

  Homo.sapiens
  cls <- columns(Homo.sapiens)
  cls
  cls <- cls[c(1,19,45)]
  kts <- keytypes(Homo.sapiens)
  kt <- kts[2]
  kts
  ks <- head(keys(Homo.sapiens, keytype=kts[2]))
  ks
  res <- select(Homo.sapiens, keys=ks, columns=cls, keytype=kt)
  head(res)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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(Homo.sapiens)
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: OrganismDbi
Loading required package: GenomicFeatures
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GO.db

Loading required package: org.Hs.eg.db

Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Homo.sapiens/Homo.sapiens.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Homo.sapiens
> ### Title: Annotation package that collates several annotation resources.
> ### Aliases: Homo.sapiens
> ### Keywords: datasets
> 
> ### ** Examples
> 
>   Homo.sapiens
OrganismDb Object:
# Includes GODb Object:  GO.db 
# With data about:  Gene Ontology 
# Includes OrgDb Object:  org.Hs.eg.db 
# Gene data about:  Homo sapiens 
# Taxonomy Id:  9606 
# Includes TxDb Object:  TxDb.Hsapiens.UCSC.hg19.knownGene 
# Transcriptome data about:  Homo sapiens 
# Based on genome:  hg19 
# The OrgDb gene id ENTREZID is mapped to the TxDb gene id GENEID .
>   cls <- columns(Homo.sapiens)
>   cls
 [1] "ACCNUM"       "ALIAS"        "CDSCHROM"     "CDSEND"       "CDSID"       
 [6] "CDSNAME"      "CDSSTART"     "CDSSTRAND"    "DEFINITION"   "ENSEMBL"     
[11] "ENSEMBLPROT"  "ENSEMBLTRANS" "ENTREZID"     "ENZYME"       "EVIDENCE"    
[16] "EVIDENCEALL"  "EXONCHROM"    "EXONEND"      "EXONID"       "EXONNAME"    
[21] "EXONRANK"     "EXONSTART"    "EXONSTRAND"   "GENEID"       "GENENAME"    
[26] "GO"           "GOALL"        "GOID"         "IPI"          "MAP"         
[31] "OMIM"         "ONTOLOGY"     "ONTOLOGYALL"  "PATH"         "PFAM"        
[36] "PMID"         "PROSITE"      "REFSEQ"       "SYMBOL"       "TERM"        
[41] "TXCHROM"      "TXEND"        "TXID"         "TXNAME"       "TXSTART"     
[46] "TXSTRAND"     "TXTYPE"       "UCSCKG"       "UNIGENE"      "UNIPROT"     
>   cls <- cls[c(1,19,45)]
>   kts <- keytypes(Homo.sapiens)
>   kt <- kts[2]
>   kts
 [1] "ACCNUM"       "ALIAS"        "CDSID"        "CDSNAME"      "DEFINITION"  
 [6] "ENSEMBL"      "ENSEMBLPROT"  "ENSEMBLTRANS" "ENTREZID"     "ENZYME"      
[11] "EVIDENCE"     "EVIDENCEALL"  "EXONID"       "EXONNAME"     "GENEID"      
[16] "GENENAME"     "GO"           "GOALL"        "GOID"         "IPI"         
[21] "MAP"          "OMIM"         "ONTOLOGY"     "ONTOLOGYALL"  "PATH"        
[26] "PFAM"         "PMID"         "PROSITE"      "REFSEQ"       "SYMBOL"      
[31] "TERM"         "TXID"         "TXNAME"       "UCSCKG"       "UNIGENE"     
[36] "UNIPROT"     
>   ks <- head(keys(Homo.sapiens, keytype=kts[2]))
>   ks
[1] "A1B"      "ABG"      "GAB"      "HYST2477" "A1BG"     "A2MD"    
>   res <- select(Homo.sapiens, keys=ks, columns=cls, keytype=kt)
'select()' returned 1:many mapping between keys and columns
>   head(res)
  ALIAS   ACCNUM EXONID  TXSTART
1   A1B AA484435 250818 58858172
2   A1B AA484435 250817 58858172
3   A1B AA484435 250816 58858172
4   A1B AA484435 250815 58858172
5   A1B AA484435 250814 58858172
6   A1B AA484435 250813 58858172
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>