Supported by Dr. Osamu Ogasawara and  providing  . |
|
Last data update: 2014.03.03 |
Basic usage of an Ensembl based annotation databaseDescriptionGet some basic information from an Ensembl based annotation package
generated with Usage
## S4 method for signature 'EnsDb'
buildQuery(x, columns=c("gene_id", "gene_biotype",
"gene_name"), filter=list(), order.by,
order.type="asc", skip.order.check=FALSE)
## S4 method for signature 'EnsDb'
dbconn(x)
EnsDb(x)
## S4 method for signature 'EnsDb'
ensemblVersion(x)
## S4 method for signature 'EnsDb'
listColumns(x, table, skip.keys=TRUE, ...)
## S4 method for signature 'EnsDb'
listGenebiotypes(x, ...)
## S4 method for signature 'EnsDb'
listTxbiotypes(x, ...)
## S4 method for signature 'EnsDb'
listTables(x, ...)
## S4 method for signature 'EnsDb'
metadata(x, ...)
## S4 method for signature 'EnsDb'
organism(object)
## S4 method for signature 'EnsDb'
seqinfo(x)
## S4 method for signature 'EnsDb'
seqlevels(x)
## S4 method for signature 'EnsDb'
updateEnsDb(x, ...)
Arguments(in alphabetic order)
Value
Objects from the ClassA connection to the respective annotation database is created upon
loading of an annotation package created with the
Slots
Methods and Functions
Author(s)Johannes Rainer See Also
Examples
library(EnsDb.Hsapiens.v75)
## Display some information:
EnsDb.Hsapiens.v75
## Show the tables along with its columns
listTables(EnsDb.Hsapiens.v75)
## For what species is this database?
organism(EnsDb.Hsapiens.v75)
## What Ensembl version if the database based on?
ensemblVersion(EnsDb.Hsapiens.v75)
## Get some more information from the database
metadata(EnsDb.Hsapiens.v75)
## Get all the sequence names.
seqlevels(EnsDb.Hsapiens.v75)
###### buildQuery
##
## Join tables gene and transcript and return gene_id and tx_id
buildQuery(EnsDb.Hsapiens.v75, columns=c("gene_id", "tx_id"))
## Get all exon_ids and transcript ids of genes encoded on chromosome Y.
buildQuery(EnsDb.Hsapiens.v75, columns=c("exon_id", "tx_id"),
filter=list(SeqnameFilter( "Y")))
## List all available gene biotypes from the database:
listGenebiotypes(EnsDb.Hsapiens.v75)
## List all available transcript biotypes:
listTxbiotypes(EnsDb.Hsapiens.v75)
## Update the EnsDb; this is in most instances not necessary at all.
updateEnsDb(EnsDb.Hsapiens.v75)
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.
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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(ensembldb)
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: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
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")'.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ensembldb/EnsDb-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: EnsDb-class
> ### Title: Basic usage of an Ensembl based annotation database
> ### Aliases: EnsDb-class EnsDb buildQuery buildQuery,EnsDb-method dbconn
> ### dbconn,EnsDb-method ensemblVersion ensemblVersion,EnsDb-method
> ### listColumns listColumns,EnsDb-method metadata metadata,EnsDb-method
> ### seqinfo seqinfo,EnsDb-method seqlevels seqlevels,EnsDb-method
> ### organism organism,EnsDb-method show show,EnsDb-method
> ### listGenebiotypes listGenebiotypes,EnsDb-method listTxbiotypes
> ### listTxbiotypes,EnsDb-method listTables listTables,EnsDb-method
> ### updateEnsDb updateEnsDb,EnsDb-method
> ### Keywords: classes
>
> ### ** Examples
>
>
> library(EnsDb.Hsapiens.v75)
>
> ## Display some information:
> EnsDb.Hsapiens.v75
EnsDb for Ensembl:
|Db type: EnsDb
|Type of Gene ID: Ensembl Gene ID
|Supporting package: ensembldb
|Db created by: ensembldb package from Bioconductor
|script_version: 0.1.2
|Creation time: Wed Mar 18 09:30:54 2015
|ensembl_version: 75
|ensembl_host: manny.i-med.ac.at
|Organism: homo_sapiens
|genome_build: GRCh37
|DBSCHEMAVERSION: 1.0
| No. of genes: 64102.
| No. of transcripts: 215647.
>
> ## Show the tables along with its columns
> listTables(EnsDb.Hsapiens.v75)
$gene
[1] "gene_id" "gene_name" "entrezid" "gene_biotype"
[5] "gene_seq_start" "gene_seq_end" "seq_name" "seq_strand"
[9] "seq_coord_system"
$tx
[1] "tx_id" "tx_biotype" "tx_seq_start" "tx_seq_end"
[5] "tx_cds_seq_start" "tx_cds_seq_end" "gene_id"
$tx2exon
[1] "tx_id" "exon_id" "exon_idx"
$exon
[1] "exon_id" "exon_seq_start" "exon_seq_end"
$chromosome
[1] "seq_name" "seq_length" "is_circular"
$metadata
[1] "name" "value"
>
> ## For what species is this database?
> organism(EnsDb.Hsapiens.v75)
[1] "Homo sapiens"
>
> ## What Ensembl version if the database based on?
> ensemblVersion(EnsDb.Hsapiens.v75)
[1] "75"
>
> ## Get some more information from the database
> metadata(EnsDb.Hsapiens.v75)
name value
1 Db type EnsDb
2 Type of Gene ID Ensembl Gene ID
3 Supporting package ensembldb
4 Db created by ensembldb package from Bioconductor
5 script_version 0.1.2
6 Creation time Wed Mar 18 09:30:54 2015
7 ensembl_version 75
8 ensembl_host manny.i-med.ac.at
9 Organism homo_sapiens
10 genome_build GRCh37
11 DBSCHEMAVERSION 1.0
>
> ## Get all the sequence names.
> seqlevels(EnsDb.Hsapiens.v75)
[1] "1" "10"
[3] "11" "12"
[5] "13" "14"
[7] "15" "16"
[9] "17" "18"
[11] "19" "2"
[13] "20" "21"
[15] "22" "3"
[17] "4" "5"
[19] "6" "7"
[21] "8" "9"
[23] "GL000191.1" "GL000192.1"
[25] "GL000193.1" "GL000194.1"
[27] "GL000195.1" "GL000196.1"
[29] "GL000199.1" "GL000201.1"
[31] "GL000204.1" "GL000205.1"
[33] "GL000209.1" "GL000211.1"
[35] "GL000212.1" "GL000213.1"
[37] "GL000215.1" "GL000216.1"
[39] "GL000218.1" "GL000219.1"
[41] "GL000220.1" "GL000221.1"
[43] "GL000222.1" "GL000223.1"
[45] "GL000224.1" "GL000225.1"
[47] "GL000228.1" "GL000229.1"
[49] "GL000230.1" "GL000231.1"
[51] "GL000233.1" "GL000236.1"
[53] "GL000237.1" "GL000240.1"
[55] "GL000241.1" "GL000242.1"
[57] "GL000243.1" "GL000247.1"
[59] "HG1007_PATCH" "HG1032_PATCH"
[61] "HG104_HG975_PATCH" "HG1063_PATCH"
[63] "HG1074_PATCH" "HG1079_PATCH"
[65] "HG1082_HG167_PATCH" "HG1091_PATCH"
[67] "HG1133_PATCH" "HG1146_PATCH"
[69] "HG115_PATCH" "HG1208_PATCH"
[71] "HG1211_PATCH" "HG122_PATCH"
[73] "HG1257_PATCH" "HG1287_PATCH"
[75] "HG1292_PATCH" "HG1293_PATCH"
[77] "HG1304_PATCH" "HG1308_PATCH"
[79] "HG1322_PATCH" "HG1350_HG959_PATCH"
[81] "HG1423_PATCH" "HG1424_PATCH"
[83] "HG1425_PATCH" "HG1426_PATCH"
[85] "HG142_HG150_NOVEL_TEST" "HG1433_PATCH"
[87] "HG1434_PATCH" "HG1435_PATCH"
[89] "HG1436_HG1432_PATCH" "HG1437_PATCH"
[91] "HG1438_PATCH" "HG1439_PATCH"
[93] "HG1440_PATCH" "HG1441_PATCH"
[95] "HG1442_PATCH" "HG1443_HG1444_PATCH"
[97] "HG144_PATCH" "HG1453_PATCH"
[99] "HG1458_PATCH" "HG1459_PATCH"
[101] "HG1462_PATCH" "HG1463_PATCH"
[103] "HG1472_PATCH" "HG1479_PATCH"
[105] "HG1486_PATCH" "HG1487_PATCH"
[107] "HG1488_PATCH" "HG1490_PATCH"
[109] "HG1497_PATCH" "HG14_PATCH"
[111] "HG1500_PATCH" "HG1501_PATCH"
[113] "HG1502_PATCH" "HG151_NOVEL_TEST"
[115] "HG1591_PATCH" "HG1592_PATCH"
[117] "HG1595_PATCH" "HG1699_PATCH"
[119] "HG174_HG254_PATCH" "HG183_PATCH"
[121] "HG185_PATCH" "HG186_PATCH"
[123] "HG193_PATCH" "HG19_PATCH"
[125] "HG237_PATCH" "HG243_PATCH"
[127] "HG256_PATCH" "HG271_PATCH"
[129] "HG27_PATCH" "HG280_PATCH"
[131] "HG281_PATCH" "HG299_PATCH"
[133] "HG29_PATCH" "HG305_PATCH"
[135] "HG306_PATCH" "HG311_PATCH"
[137] "HG325_PATCH" "HG329_PATCH"
[139] "HG339_PATCH" "HG344_PATCH"
[141] "HG348_PATCH" "HG357_PATCH"
[143] "HG375_PATCH" "HG385_PATCH"
[145] "HG388_HG400_PATCH" "HG414_PATCH"
[147] "HG417_PATCH" "HG418_PATCH"
[149] "HG444_PATCH" "HG480_HG481_PATCH"
[151] "HG497_PATCH" "HG506_HG507_HG1000_PATCH"
[153] "HG50_PATCH" "HG531_PATCH"
[155] "HG536_PATCH" "HG544_PATCH"
[157] "HG686_PATCH" "HG706_PATCH"
[159] "HG729_PATCH" "HG730_PATCH"
[161] "HG736_PATCH" "HG745_PATCH"
[163] "HG747_PATCH" "HG748_PATCH"
[165] "HG75_PATCH" "HG79_PATCH"
[167] "HG7_PATCH" "HG858_PATCH"
[169] "HG865_PATCH" "HG871_PATCH"
[171] "HG873_PATCH" "HG883_PATCH"
[173] "HG905_PATCH" "HG944_PATCH"
[175] "HG946_PATCH" "HG953_PATCH"
[177] "HG957_PATCH" "HG962_PATCH"
[179] "HG971_PATCH" "HG979_PATCH"
[181] "HG987_PATCH" "HG989_PATCH"
[183] "HG990_PATCH" "HG991_PATCH"
[185] "HG996_PATCH" "HG998_1_PATCH"
[187] "HG998_2_PATCH" "HG999_1_PATCH"
[189] "HG999_2_PATCH" "HSCHR10_1_CTG2"
[191] "HSCHR10_1_CTG5" "HSCHR12_1_CTG1"
[193] "HSCHR12_1_CTG2_1" "HSCHR12_1_CTG5"
[195] "HSCHR12_2_CTG2" "HSCHR12_2_CTG2_1"
[197] "HSCHR12_3_CTG2_1" "HSCHR15_1_CTG4"
[199] "HSCHR15_1_CTG8" "HSCHR16_1_CTG3_1"
[201] "HSCHR16_2_CTG3_1" "HSCHR17_1"
[203] "HSCHR17_1_CTG1" "HSCHR17_1_CTG4"
[205] "HSCHR17_2_CTG4" "HSCHR17_3_CTG4"
[207] "HSCHR17_4_CTG4" "HSCHR17_5_CTG4"
[209] "HSCHR17_6_CTG4" "HSCHR18_1_CTG1_1"
[211] "HSCHR18_1_CTG2_1" "HSCHR18_2_CTG2"
[213] "HSCHR18_2_CTG2_1" "HSCHR19LRC_COX1_CTG1"
[215] "HSCHR19LRC_COX2_CTG1" "HSCHR19LRC_LRC_I_CTG1"
[217] "HSCHR19LRC_LRC_J_CTG1" "HSCHR19LRC_LRC_S_CTG1"
[219] "HSCHR19LRC_LRC_T_CTG1" "HSCHR19LRC_PGF1_CTG1"
[221] "HSCHR19LRC_PGF2_CTG1" "HSCHR19_1_CTG3"
[223] "HSCHR19_1_CTG3_1" "HSCHR19_2_CTG3"
[225] "HSCHR19_3_CTG3" "HSCHR1_1_CTG31"
[227] "HSCHR1_2_CTG31" "HSCHR1_3_CTG31"
[229] "HSCHR20_1_CTG1" "HSCHR21_2_CTG1_1"
[231] "HSCHR21_3_CTG1_1" "HSCHR21_4_CTG1_1"
[233] "HSCHR22_1_CTG1" "HSCHR22_1_CTG2"
[235] "HSCHR22_2_CTG1" "HSCHR2_1_CTG1"
[237] "HSCHR2_1_CTG12" "HSCHR2_2_CTG12"
[239] "HSCHR3_1_CTG1" "HSCHR3_1_CTG2_1"
[241] "HSCHR4_1" "HSCHR4_1_CTG12"
[243] "HSCHR4_1_CTG6" "HSCHR4_2_CTG9"
[245] "HSCHR5_1_CTG1" "HSCHR5_1_CTG2"
[247] "HSCHR5_1_CTG5" "HSCHR5_2_CTG1"
[249] "HSCHR5_3_CTG1" "HSCHR6_1_CTG5"
[251] "HSCHR6_MHC_APD" "HSCHR6_MHC_COX"
[253] "HSCHR6_MHC_DBB" "HSCHR6_MHC_MANN"
[255] "HSCHR6_MHC_MCF" "HSCHR6_MHC_QBL"
[257] "HSCHR6_MHC_SSTO" "HSCHR7_1_CTG6"
[259] "HSCHR9_1_CTG1" "HSCHR9_1_CTG35"
[261] "HSCHR9_2_CTG35" "HSCHR9_3_CTG35"
[263] "LRG_123" "LRG_162"
[265] "LRG_183" "LRG_187"
[267] "LRG_239" "LRG_311"
[269] "LRG_415" "LRG_93"
[271] "MT" "X"
[273] "Y"
>
> ###### buildQuery
> ##
> ## Join tables gene and transcript and return gene_id and tx_id
> buildQuery(EnsDb.Hsapiens.v75, columns=c("gene_id", "tx_id"))
[1] "select distinct tx.tx_id,tx.gene_id from tx"
>
>
> ## Get all exon_ids and transcript ids of genes encoded on chromosome Y.
> buildQuery(EnsDb.Hsapiens.v75, columns=c("exon_id", "tx_id"),
+ filter=list(SeqnameFilter( "Y")))
[1] "select distinct gene.seq_name,tx2exon.tx_id,tx2exon.exon_id from gene join tx on (gene.gene_id=tx.gene_id) join tx2exon on (tx.tx_id=tx2exon.tx_id) where gene.seq_name = 'Y'"
>
> ## List all available gene biotypes from the database:
> listGenebiotypes(EnsDb.Hsapiens.v75)
[1] "protein_coding" "pseudogene"
[3] "processed_transcript" "antisense"
[5] "lincRNA" "polymorphic_pseudogene"
[7] "IG_V_pseudogene" "IG_V_gene"
[9] "sense_overlapping" "sense_intronic"
[11] "TR_V_gene" "misc_RNA"
[13] "snRNA" "miRNA"
[15] "snoRNA" "rRNA"
[17] "Mt_tRNA" "Mt_rRNA"
[19] "IG_C_gene" "IG_J_gene"
[21] "TR_J_gene" "TR_C_gene"
[23] "TR_V_pseudogene" "TR_J_pseudogene"
[25] "IG_D_gene" "IG_C_pseudogene"
[27] "TR_D_gene" "IG_J_pseudogene"
[29] "3prime_overlapping_ncrna" "processed_pseudogene"
[31] "LRG_gene"
>
> ## List all available transcript biotypes:
> listTxbiotypes(EnsDb.Hsapiens.v75)
[1] "protein_coding" "processed_transcript"
[3] "retained_intron" "nonsense_mediated_decay"
[5] "unitary_pseudogene" "non_stop_decay"
[7] "unprocessed_pseudogene" "processed_pseudogene"
[9] "transcribed_unprocessed_pseudogene" "antisense"
[11] "lincRNA" "polymorphic_pseudogene"
[13] "transcribed_processed_pseudogene" "miRNA"
[15] "pseudogene" "IG_V_pseudogene"
[17] "snoRNA" "IG_V_gene"
[19] "sense_overlapping" "sense_intronic"
[21] "TR_V_gene" "snRNA"
[23] "misc_RNA" "rRNA"
[25] "Mt_tRNA" "Mt_rRNA"
[27] "IG_C_gene" "IG_J_gene"
[29] "TR_J_gene" "TR_C_gene"
[31] "TR_V_pseudogene" "TR_J_pseudogene"
[33] "IG_D_gene" "IG_C_pseudogene"
[35] "TR_D_gene" "IG_J_pseudogene"
[37] "3prime_overlapping_ncrna" "translated_processed_pseudogene"
[39] "LRG_gene"
>
> ## Update the EnsDb; this is in most instances not necessary at all.
> updateEnsDb(EnsDb.Hsapiens.v75)
EnsDb for Ensembl:
|Db type: EnsDb
|Type of Gene ID: Ensembl Gene ID
|Supporting package: ensembldb
|Db created by: ensembldb package from Bioconductor
|script_version: 0.1.2
|Creation time: Wed Mar 18 09:30:54 2015
|ensembl_version: 75
|ensembl_host: manny.i-med.ac.at
|Organism: homo_sapiens
|genome_build: GRCh37
|DBSCHEMAVERSION: 1.0
| No. of genes: 64102.
| No. of transcripts: 215647.
>
>
>
>
>
>
> dev.off()
null device
1
>
|
Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and