EnsDb-class.RdThe EnsDb class provides access to an Ensembl-based annotation
package. This help page describes functions to get some basic
informations from such an object.
# S4 method for EnsDb
dbconn(x)
# S4 method for EnsDb
ensemblVersion(x)
# S4 method for EnsDb
listColumns(x, table, skip.keys = TRUE, metadata = FALSE, ...)
# S4 method for EnsDb
listGenebiotypes(x, ...)
# S4 method for EnsDb
listTxbiotypes(x, ...)
# S4 method for EnsDb
listTables(x, ...)
# S4 method for EnsDb
metadata(x, ...)
# S4 method for EnsDb
organism(object)
# S4 method for EnsDb
returnFilterColumns(x)
# S4 method for EnsDb
returnFilterColumns(x)
# S4 method for EnsDb
returnFilterColumns(x) <- value
# S4 method for EnsDb
seqinfo(x)
# S4 method for EnsDb
seqlevels(x)
# S4 method for EnsDb
updateEnsDb(x, ...)A connection to the respective annotation database is created upon
loading of an annotation package created with the
makeEnsembldbPackage function. In addition, the
EnsDb constructor specifying the SQLite database file can be
called to generate an instance of the object (see
makeEnsemblSQLiteFromTables for an example).
(in alphabetic order)
Additional arguments. Not used.
For listColumns: whether columns from the
metadata database column should also be returned. Defaults to
metadata = FALSE.
For organism: an EnsDb instance.
for listColumns: whether primary and foreign keys (not
being e.g. "gene_id" or alike) should be returned or not. By
default these will not be returned.
For listColumns: optionally specify the table name(s) for
which the columns should be returned.
For returnFilterColumns: a logical of length one specifying
whether columns that are used for eventual filters should also be
returned.
An EnsDb instance.
Object of class "DBIConnection": the
connection to the database.
Named list of database table columns with the names being the database table names. The tables are ordered by their degree, i.e. the number of other tables they can be joined with.
Internal list storing user-defined properties. Should not be directly accessed.
Returns the connection to the internal SQL database.
Returns the Ensembl version on which the package was built.
Lists all columns of all tables in the database, or, if
table is specified, of the respective table.
Lists all gene biotypes defined in the database.
Lists all transcript biotypes defined in the database.
Returns a named list of database table columns (names of the list being the database table names).
Returns a data.frame with the metadata information from the
database, i.e. informations about the Ensembl version or Genome
build the database was build upon.
Returns the organism name (e.g. "homo_sapiens").
Get or set the option which results in columns that are used for
eventually specified filters to be added as result columns. The
default value is TRUE (i.e. filter columns are returned).
Returns the sequence/chromosome information from the database.
Returns the chromosome/sequence names that are available in the database.
Displays some informations from the database.
Updates the EnsDb object to the most recent implementation.
connectionThe SQL connection to the RSQLite database.
EnsDbAn EnsDb instance.
lengthOfA named integer vector with the length of the genes or transcripts.
listColumnsA character vector with the column names.
listGenebiotypesA character vector with the biotypes of the genes in the database.
listTxbiotypesA character vector with the biotypes of the transcripts in the database.
listTablesA list with the names corresponding to the database table names and the elements being the attribute (column) names of the table.
metadataA data.frame.
organismA character string.
returnFilterColumnsA logical of length 1.
seqinfoA Seqinfo class.
updateEnsDbA EnsDb object.
While a column named "tx_name" is listed by the
listTables and listColumns method, no such column is
present in the database. Transcript names returned by the methods are
actually the transcript IDs. This virtual column was only
introduced to be compliant with TxDb objects (which provide
transcript names).
EnsDb,
makeEnsembldbPackage,
exonsBy, genes,
transcripts,
makeEnsemblSQLiteFromTables
addFilter for globally adding filters to an EnsDb
object.
library(EnsDb.Hsapiens.v86)
## Display some information:
EnsDb.Hsapiens.v86
#> EnsDb for Ensembl:
#> |Backend: SQLite
#> |Db type: EnsDb
#> |Type of Gene ID: Ensembl Gene ID
#> |Supporting package: ensembldb
#> |Db created by: ensembldb package from Bioconductor
#> |script_version: 0.3.0
#> |Creation time: Thu May 18 16:32:27 2017
#> |ensembl_version: 86
#> |ensembl_host: localhost
#> |Organism: homo_sapiens
#> |taxonomy_id: 9606
#> |genome_build: GRCh38
#> |DBSCHEMAVERSION: 2.0
#> | No. of genes: 63970.
#> | No. of transcripts: 216741.
#> |Protein data available.
## Show the tables along with its columns
listTables(EnsDb.Hsapiens.v86)
#> $gene
#> [1] "gene_id" "gene_name" "gene_biotype" "gene_seq_start"
#> [5] "gene_seq_end" "seq_name" "seq_strand" "seq_coord_system"
#> [9] "symbol"
#>
#> $tx
#> [1] "tx_id" "tx_biotype" "tx_seq_start" "tx_seq_end"
#> [5] "tx_cds_seq_start" "tx_cds_seq_end" "gene_id" "tx_name"
#>
#> $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"
#>
#> $protein
#> [1] "tx_id" "protein_id" "protein_sequence"
#>
#> $uniprot
#> [1] "protein_id" "uniprot_id" "uniprot_db"
#> [4] "uniprot_mapping_type"
#>
#> $protein_domain
#> [1] "protein_id" "protein_domain_id" "protein_domain_source"
#> [4] "interpro_accession" "prot_dom_start" "prot_dom_end"
#>
#> $entrezgene
#> [1] "gene_id" "entrezid"
#>
#> $metadata
#> [1] "name" "value"
#>
## For what species is this database?
organism(EnsDb.Hsapiens.v86)
#> [1] "Homo sapiens"
## What Ensembl version if the database based on?
ensemblVersion(EnsDb.Hsapiens.v86)
#> [1] "86"
## Get some more information from the database
metadata(EnsDb.Hsapiens.v86)
#> 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 0.3.0
#> 6 Creation time Thu May 18 16:32:27 2017
#> 7 ensembl_version 86
#> 8 ensembl_host localhost
#> 9 Organism homo_sapiens
#> 10 taxonomy_id 9606
#> 11 genome_build GRCh38
#> 12 DBSCHEMAVERSION 2.0
## Get all the sequence names.
seqlevels(EnsDb.Hsapiens.v86)
#> [1] "1"
#> [2] "10"
#> [3] "11"
#> [4] "12"
#> [5] "13"
#> [6] "14"
#> [7] "15"
#> [8] "16"
#> [9] "17"
#> [10] "18"
#> [11] "19"
#> [12] "2"
#> [13] "20"
#> [14] "21"
#> [15] "22"
#> [16] "3"
#> [17] "4"
#> [18] "5"
#> [19] "6"
#> [20] "7"
#> [21] "8"
#> [22] "9"
#> [23] "CHR_HG107_PATCH"
#> [24] "CHR_HG126_PATCH"
#> [25] "CHR_HG1311_PATCH"
#> [26] "CHR_HG1342_HG2282_PATCH"
#> [27] "CHR_HG1362_PATCH"
#> [28] "CHR_HG142_HG150_NOVEL_TEST"
#> [29] "CHR_HG151_NOVEL_TEST"
#> [30] "CHR_HG1651_PATCH"
#> [31] "CHR_HG1832_PATCH"
#> [32] "CHR_HG2021_PATCH"
#> [33] "CHR_HG2022_PATCH"
#> [34] "CHR_HG2023_PATCH"
#> [35] "CHR_HG2030_PATCH"
#> [36] "CHR_HG2058_PATCH"
#> [37] "CHR_HG2062_PATCH"
#> [38] "CHR_HG2063_PATCH"
#> [39] "CHR_HG2066_PATCH"
#> [40] "CHR_HG2072_PATCH"
#> [41] "CHR_HG2095_PATCH"
#> [42] "CHR_HG2104_PATCH"
#> [43] "CHR_HG2116_PATCH"
#> [44] "CHR_HG2128_PATCH"
#> [45] "CHR_HG2191_PATCH"
#> [46] "CHR_HG2213_PATCH"
#> [47] "CHR_HG2217_PATCH"
#> [48] "CHR_HG2232_PATCH"
#> [49] "CHR_HG2233_PATCH"
#> [50] "CHR_HG2235_PATCH"
#> [51] "CHR_HG2239_PATCH"
#> [52] "CHR_HG2247_PATCH"
#> [53] "CHR_HG2249_PATCH"
#> [54] "CHR_HG2288_HG2289_PATCH"
#> [55] "CHR_HG2290_PATCH"
#> [56] "CHR_HG2291_PATCH"
#> [57] "CHR_HG2334_PATCH"
#> [58] "CHR_HG26_PATCH"
#> [59] "CHR_HG986_PATCH"
#> [60] "CHR_HSCHR10_1_CTG1"
#> [61] "CHR_HSCHR10_1_CTG2"
#> [62] "CHR_HSCHR10_1_CTG3"
#> [63] "CHR_HSCHR10_1_CTG4"
#> [64] "CHR_HSCHR10_1_CTG6"
#> [65] "CHR_HSCHR11_1_CTG1_2"
#> [66] "CHR_HSCHR11_1_CTG5"
#> [67] "CHR_HSCHR11_1_CTG6"
#> [68] "CHR_HSCHR11_1_CTG7"
#> [69] "CHR_HSCHR11_1_CTG8"
#> [70] "CHR_HSCHR11_2_CTG1"
#> [71] "CHR_HSCHR11_2_CTG1_1"
#> [72] "CHR_HSCHR11_3_CTG1"
#> [73] "CHR_HSCHR12_1_CTG1"
#> [74] "CHR_HSCHR12_1_CTG2_1"
#> [75] "CHR_HSCHR12_2_CTG1"
#> [76] "CHR_HSCHR12_2_CTG2"
#> [77] "CHR_HSCHR12_2_CTG2_1"
#> [78] "CHR_HSCHR12_3_CTG2"
#> [79] "CHR_HSCHR12_3_CTG2_1"
#> [80] "CHR_HSCHR12_4_CTG2"
#> [81] "CHR_HSCHR12_4_CTG2_1"
#> [82] "CHR_HSCHR12_5_CTG2"
#> [83] "CHR_HSCHR12_5_CTG2_1"
#> [84] "CHR_HSCHR12_6_CTG2_1"
#> [85] "CHR_HSCHR13_1_CTG1"
#> [86] "CHR_HSCHR13_1_CTG3"
#> [87] "CHR_HSCHR13_1_CTG5"
#> [88] "CHR_HSCHR13_1_CTG8"
#> [89] "CHR_HSCHR14_1_CTG1"
#> [90] "CHR_HSCHR14_2_CTG1"
#> [91] "CHR_HSCHR14_3_CTG1"
#> [92] "CHR_HSCHR14_7_CTG1"
#> [93] "CHR_HSCHR15_1_CTG1"
#> [94] "CHR_HSCHR15_1_CTG3"
#> [95] "CHR_HSCHR15_1_CTG8"
#> [96] "CHR_HSCHR15_2_CTG3"
#> [97] "CHR_HSCHR15_2_CTG8"
#> [98] "CHR_HSCHR15_3_CTG3"
#> [99] "CHR_HSCHR15_3_CTG8"
#> [100] "CHR_HSCHR15_4_CTG8"
#> [101] "CHR_HSCHR15_5_CTG8"
#> [102] "CHR_HSCHR15_6_CTG8"
#> [103] "CHR_HSCHR16_1_CTG1"
#> [104] "CHR_HSCHR16_1_CTG3_1"
#> [105] "CHR_HSCHR16_2_CTG3_1"
#> [106] "CHR_HSCHR16_3_CTG1"
#> [107] "CHR_HSCHR16_4_CTG1"
#> [108] "CHR_HSCHR16_4_CTG3_1"
#> [109] "CHR_HSCHR16_5_CTG1"
#> [110] "CHR_HSCHR16_CTG2"
#> [111] "CHR_HSCHR17_10_CTG4"
#> [112] "CHR_HSCHR17_1_CTG1"
#> [113] "CHR_HSCHR17_1_CTG2"
#> [114] "CHR_HSCHR17_1_CTG4"
#> [115] "CHR_HSCHR17_1_CTG5"
#> [116] "CHR_HSCHR17_1_CTG9"
#> [117] "CHR_HSCHR17_2_CTG1"
#> [118] "CHR_HSCHR17_2_CTG2"
#> [119] "CHR_HSCHR17_2_CTG4"
#> [120] "CHR_HSCHR17_2_CTG5"
#> [121] "CHR_HSCHR17_3_CTG2"
#> [122] "CHR_HSCHR17_3_CTG4"
#> [123] "CHR_HSCHR17_4_CTG4"
#> [124] "CHR_HSCHR17_5_CTG4"
#> [125] "CHR_HSCHR17_6_CTG4"
#> [126] "CHR_HSCHR17_7_CTG4"
#> [127] "CHR_HSCHR17_8_CTG4"
#> [128] "CHR_HSCHR17_9_CTG4"
#> [129] "CHR_HSCHR18_1_CTG1_1"
#> [130] "CHR_HSCHR18_1_CTG2_1"
#> [131] "CHR_HSCHR18_2_CTG1_1"
#> [132] "CHR_HSCHR18_2_CTG2"
#> [133] "CHR_HSCHR18_2_CTG2_1"
#> [134] "CHR_HSCHR18_3_CTG2_1"
#> [135] "CHR_HSCHR18_5_CTG1_1"
#> [136] "CHR_HSCHR18_ALT21_CTG2_1"
#> [137] "CHR_HSCHR18_ALT2_CTG2_1"
#> [138] "CHR_HSCHR19KIR_ABC08_A1_HAP_CTG3_1"
#> [139] "CHR_HSCHR19KIR_ABC08_AB_HAP_C_P_CTG3_1"
#> [140] "CHR_HSCHR19KIR_ABC08_AB_HAP_T_P_CTG3_1"
#> [141] "CHR_HSCHR19KIR_FH05_A_HAP_CTG3_1"
#> [142] "CHR_HSCHR19KIR_FH05_B_HAP_CTG3_1"
#> [143] "CHR_HSCHR19KIR_FH06_A_HAP_CTG3_1"
#> [144] "CHR_HSCHR19KIR_FH06_BA1_HAP_CTG3_1"
#> [145] "CHR_HSCHR19KIR_FH08_A_HAP_CTG3_1"
#> [146] "CHR_HSCHR19KIR_FH08_BAX_HAP_CTG3_1"
#> [147] "CHR_HSCHR19KIR_FH13_A_HAP_CTG3_1"
#> [148] "CHR_HSCHR19KIR_FH13_BA2_HAP_CTG3_1"
#> [149] "CHR_HSCHR19KIR_FH15_A_HAP_CTG3_1"
#> [150] "CHR_HSCHR19KIR_FH15_B_HAP_CTG3_1"
#> [151] "CHR_HSCHR19KIR_G085_A_HAP_CTG3_1"
#> [152] "CHR_HSCHR19KIR_G085_BA1_HAP_CTG3_1"
#> [153] "CHR_HSCHR19KIR_G248_A_HAP_CTG3_1"
#> [154] "CHR_HSCHR19KIR_G248_BA2_HAP_CTG3_1"
#> [155] "CHR_HSCHR19KIR_GRC212_AB_HAP_CTG3_1"
#> [156] "CHR_HSCHR19KIR_GRC212_BA1_HAP_CTG3_1"
#> [157] "CHR_HSCHR19KIR_LUCE_A_HAP_CTG3_1"
#> [158] "CHR_HSCHR19KIR_LUCE_BDEL_HAP_CTG3_1"
#> [159] "CHR_HSCHR19KIR_RP5_B_HAP_CTG3_1"
#> [160] "CHR_HSCHR19KIR_RSH_A_HAP_CTG3_1"
#> [161] "CHR_HSCHR19KIR_RSH_BA2_HAP_CTG3_1"
#> [162] "CHR_HSCHR19KIR_T7526_A_HAP_CTG3_1"
#> [163] "CHR_HSCHR19KIR_T7526_BDEL_HAP_CTG3_1"
#> [164] "CHR_HSCHR19LRC_COX1_CTG3_1"
#> [165] "CHR_HSCHR19LRC_COX2_CTG3_1"
#> [166] "CHR_HSCHR19LRC_LRC_I_CTG3_1"
#> [167] "CHR_HSCHR19LRC_LRC_J_CTG3_1"
#> [168] "CHR_HSCHR19LRC_LRC_S_CTG3_1"
#> [169] "CHR_HSCHR19LRC_LRC_T_CTG3_1"
#> [170] "CHR_HSCHR19LRC_PGF1_CTG3_1"
#> [171] "CHR_HSCHR19LRC_PGF2_CTG3_1"
#> [172] "CHR_HSCHR19_1_CTG2"
#> [173] "CHR_HSCHR19_1_CTG3_1"
#> [174] "CHR_HSCHR19_2_CTG2"
#> [175] "CHR_HSCHR19_2_CTG3_1"
#> [176] "CHR_HSCHR19_3_CTG2"
#> [177] "CHR_HSCHR19_3_CTG3_1"
#> [178] "CHR_HSCHR19_4_CTG2"
#> [179] "CHR_HSCHR19_4_CTG3_1"
#> [180] "CHR_HSCHR19_5_CTG2"
#> [181] "CHR_HSCHR1_1_CTG11"
#> [182] "CHR_HSCHR1_1_CTG3"
#> [183] "CHR_HSCHR1_1_CTG31"
#> [184] "CHR_HSCHR1_1_CTG32_1"
#> [185] "CHR_HSCHR1_2_CTG3"
#> [186] "CHR_HSCHR1_2_CTG31"
#> [187] "CHR_HSCHR1_2_CTG32_1"
#> [188] "CHR_HSCHR1_3_CTG3"
#> [189] "CHR_HSCHR1_3_CTG31"
#> [190] "CHR_HSCHR1_3_CTG32_1"
#> [191] "CHR_HSCHR1_4_CTG3"
#> [192] "CHR_HSCHR1_4_CTG31"
#> [193] "CHR_HSCHR1_5_CTG3"
#> [194] "CHR_HSCHR1_5_CTG32_1"
#> [195] "CHR_HSCHR1_ALT2_1_CTG32_1"
#> [196] "CHR_HSCHR20_1_CTG1"
#> [197] "CHR_HSCHR20_1_CTG2"
#> [198] "CHR_HSCHR20_1_CTG3"
#> [199] "CHR_HSCHR20_1_CTG4"
#> [200] "CHR_HSCHR21_2_CTG1_1"
#> [201] "CHR_HSCHR21_3_CTG1_1"
#> [202] "CHR_HSCHR21_4_CTG1_1"
#> [203] "CHR_HSCHR21_5_CTG2"
#> [204] "CHR_HSCHR21_6_CTG1_1"
#> [205] "CHR_HSCHR21_8_CTG1_1"
#> [206] "CHR_HSCHR22_1_CTG1"
#> [207] "CHR_HSCHR22_1_CTG2"
#> [208] "CHR_HSCHR22_1_CTG3"
#> [209] "CHR_HSCHR22_1_CTG4"
#> [210] "CHR_HSCHR22_1_CTG5"
#> [211] "CHR_HSCHR22_1_CTG6"
#> [212] "CHR_HSCHR22_1_CTG7"
#> [213] "CHR_HSCHR22_2_CTG1"
#> [214] "CHR_HSCHR22_3_CTG1"
#> [215] "CHR_HSCHR22_4_CTG1"
#> [216] "CHR_HSCHR22_5_CTG1"
#> [217] "CHR_HSCHR22_6_CTG1"
#> [218] "CHR_HSCHR22_7_CTG1"
#> [219] "CHR_HSCHR22_8_CTG1"
#> [220] "CHR_HSCHR2_1_CTG1"
#> [221] "CHR_HSCHR2_1_CTG15"
#> [222] "CHR_HSCHR2_1_CTG5"
#> [223] "CHR_HSCHR2_1_CTG7"
#> [224] "CHR_HSCHR2_1_CTG7_2"
#> [225] "CHR_HSCHR2_2_CTG1"
#> [226] "CHR_HSCHR2_2_CTG15"
#> [227] "CHR_HSCHR2_2_CTG7"
#> [228] "CHR_HSCHR2_2_CTG7_2"
#> [229] "CHR_HSCHR2_3_CTG1"
#> [230] "CHR_HSCHR2_3_CTG15"
#> [231] "CHR_HSCHR2_3_CTG7_2"
#> [232] "CHR_HSCHR2_4_CTG1"
#> [233] "CHR_HSCHR2_6_CTG7_2"
#> [234] "CHR_HSCHR3_1_CTG1"
#> [235] "CHR_HSCHR3_1_CTG2_1"
#> [236] "CHR_HSCHR3_1_CTG3"
#> [237] "CHR_HSCHR3_2_CTG2_1"
#> [238] "CHR_HSCHR3_2_CTG3"
#> [239] "CHR_HSCHR3_3_CTG1"
#> [240] "CHR_HSCHR3_3_CTG3"
#> [241] "CHR_HSCHR3_4_CTG2_1"
#> [242] "CHR_HSCHR3_4_CTG3"
#> [243] "CHR_HSCHR3_5_CTG2_1"
#> [244] "CHR_HSCHR3_5_CTG3"
#> [245] "CHR_HSCHR3_6_CTG3"
#> [246] "CHR_HSCHR3_7_CTG3"
#> [247] "CHR_HSCHR3_8_CTG3"
#> [248] "CHR_HSCHR3_9_CTG3"
#> [249] "CHR_HSCHR4_11_CTG12"
#> [250] "CHR_HSCHR4_1_CTG12"
#> [251] "CHR_HSCHR4_1_CTG4"
#> [252] "CHR_HSCHR4_1_CTG6"
#> [253] "CHR_HSCHR4_1_CTG9"
#> [254] "CHR_HSCHR4_2_CTG12"
#> [255] "CHR_HSCHR4_2_CTG4"
#> [256] "CHR_HSCHR4_3_CTG12"
#> [257] "CHR_HSCHR4_4_CTG12"
#> [258] "CHR_HSCHR4_5_CTG12"
#> [259] "CHR_HSCHR4_6_CTG12"
#> [260] "CHR_HSCHR4_7_CTG12"
#> [261] "CHR_HSCHR4_8_CTG12"
#> [262] "CHR_HSCHR4_9_CTG12"
#> [263] "CHR_HSCHR5_1_CTG1"
#> [264] "CHR_HSCHR5_1_CTG1_1"
#> [265] "CHR_HSCHR5_1_CTG5"
#> [266] "CHR_HSCHR5_2_CTG1"
#> [267] "CHR_HSCHR5_2_CTG1_1"
#> [268] "CHR_HSCHR5_2_CTG5"
#> [269] "CHR_HSCHR5_3_CTG1"
#> [270] "CHR_HSCHR5_3_CTG5"
#> [271] "CHR_HSCHR5_4_CTG1"
#> [272] "CHR_HSCHR5_4_CTG1_1"
#> [273] "CHR_HSCHR5_5_CTG1"
#> [274] "CHR_HSCHR5_6_CTG1"
#> [275] "CHR_HSCHR5_7_CTG1"
#> [276] "CHR_HSCHR6_1_CTG10"
#> [277] "CHR_HSCHR6_1_CTG2"
#> [278] "CHR_HSCHR6_1_CTG3"
#> [279] "CHR_HSCHR6_1_CTG4"
#> [280] "CHR_HSCHR6_1_CTG5"
#> [281] "CHR_HSCHR6_1_CTG6"
#> [282] "CHR_HSCHR6_1_CTG7"
#> [283] "CHR_HSCHR6_1_CTG8"
#> [284] "CHR_HSCHR6_1_CTG9"
#> [285] "CHR_HSCHR6_8_CTG1"
#> [286] "CHR_HSCHR6_MHC_APD_CTG1"
#> [287] "CHR_HSCHR6_MHC_COX_CTG1"
#> [288] "CHR_HSCHR6_MHC_DBB_CTG1"
#> [289] "CHR_HSCHR6_MHC_MANN_CTG1"
#> [290] "CHR_HSCHR6_MHC_MCF_CTG1"
#> [291] "CHR_HSCHR6_MHC_QBL_CTG1"
#> [292] "CHR_HSCHR6_MHC_SSTO_CTG1"
#> [293] "CHR_HSCHR7_1_CTG1"
#> [294] "CHR_HSCHR7_1_CTG4_4"
#> [295] "CHR_HSCHR7_1_CTG6"
#> [296] "CHR_HSCHR7_1_CTG7"
#> [297] "CHR_HSCHR7_2_CTG1"
#> [298] "CHR_HSCHR7_2_CTG4_4"
#> [299] "CHR_HSCHR7_2_CTG6"
#> [300] "CHR_HSCHR7_2_CTG7"
#> [301] "CHR_HSCHR7_3_CTG6"
#> [302] "CHR_HSCHR8_1_CTG1"
#> [303] "CHR_HSCHR8_1_CTG6"
#> [304] "CHR_HSCHR8_1_CTG7"
#> [305] "CHR_HSCHR8_2_CTG1"
#> [306] "CHR_HSCHR8_2_CTG7"
#> [307] "CHR_HSCHR8_3_CTG1"
#> [308] "CHR_HSCHR8_3_CTG7"
#> [309] "CHR_HSCHR8_4_CTG1"
#> [310] "CHR_HSCHR8_4_CTG7"
#> [311] "CHR_HSCHR8_5_CTG1"
#> [312] "CHR_HSCHR8_5_CTG7"
#> [313] "CHR_HSCHR8_6_CTG1"
#> [314] "CHR_HSCHR8_7_CTG1"
#> [315] "CHR_HSCHR8_8_CTG1"
#> [316] "CHR_HSCHR8_9_CTG1"
#> [317] "CHR_HSCHR9_1_CTG1"
#> [318] "CHR_HSCHR9_1_CTG2"
#> [319] "CHR_HSCHR9_1_CTG3"
#> [320] "CHR_HSCHR9_1_CTG4"
#> [321] "CHR_HSCHR9_1_CTG5"
#> [322] "CHR_HSCHR9_1_CTG6"
#> [323] "CHR_HSCHRX_1_CTG3"
#> [324] "CHR_HSCHRX_2_CTG12"
#> [325] "CHR_HSCHRX_2_CTG3"
#> [326] "GL000009.2"
#> [327] "GL000194.1"
#> [328] "GL000195.1"
#> [329] "GL000205.2"
#> [330] "GL000213.1"
#> [331] "GL000216.2"
#> [332] "GL000218.1"
#> [333] "GL000219.1"
#> [334] "GL000220.1"
#> [335] "GL000225.1"
#> [336] "KI270442.1"
#> [337] "KI270711.1"
#> [338] "KI270713.1"
#> [339] "KI270721.1"
#> [340] "KI270726.1"
#> [341] "KI270727.1"
#> [342] "KI270728.1"
#> [343] "KI270731.1"
#> [344] "KI270733.1"
#> [345] "KI270734.1"
#> [346] "KI270744.1"
#> [347] "KI270750.1"
#> [348] "LRG_183"
#> [349] "LRG_187"
#> [350] "LRG_239"
#> [351] "LRG_311"
#> [352] "LRG_721"
#> [353] "LRG_741"
#> [354] "LRG_93"
#> [355] "MT"
#> [356] "X"
#> [357] "Y"
## List all available gene biotypes from the database:
listGenebiotypes(EnsDb.Hsapiens.v86)
#> [1] "protein_coding" "unitary_pseudogene"
#> [3] "unprocessed_pseudogene" "processed_pseudogene"
#> [5] "processed_transcript" "transcribed_unprocessed_pseudogene"
#> [7] "antisense" "transcribed_unitary_pseudogene"
#> [9] "polymorphic_pseudogene" "lincRNA"
#> [11] "sense_intronic" "transcribed_processed_pseudogene"
#> [13] "sense_overlapping" "IG_V_pseudogene"
#> [15] "pseudogene" "TR_V_gene"
#> [17] "3prime_overlapping_ncRNA" "IG_V_gene"
#> [19] "bidirectional_promoter_lncRNA" "snRNA"
#> [21] "miRNA" "misc_RNA"
#> [23] "snoRNA" "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" "ribozyme"
#> [35] "IG_C_pseudogene" "TR_D_gene"
#> [37] "TEC" "IG_J_pseudogene"
#> [39] "scRNA" "scaRNA"
#> [41] "vaultRNA" "sRNA"
#> [43] "macro_lncRNA" "non_coding"
#> [45] "IG_pseudogene" "LRG_gene"
## List all available transcript biotypes:
listTxbiotypes(EnsDb.Hsapiens.v86)
#> [1] "protein_coding" "processed_transcript"
#> [3] "nonsense_mediated_decay" "retained_intron"
#> [5] "unitary_pseudogene" "TEC"
#> [7] "miRNA" "misc_RNA"
#> [9] "non_stop_decay" "unprocessed_pseudogene"
#> [11] "processed_pseudogene" "transcribed_unprocessed_pseudogene"
#> [13] "lincRNA" "antisense"
#> [15] "transcribed_unitary_pseudogene" "polymorphic_pseudogene"
#> [17] "sense_intronic" "transcribed_processed_pseudogene"
#> [19] "sense_overlapping" "IG_V_pseudogene"
#> [21] "pseudogene" "TR_V_gene"
#> [23] "3prime_overlapping_ncRNA" "IG_V_gene"
#> [25] "bidirectional_promoter_lncRNA" "snRNA"
#> [27] "snoRNA" "rRNA"
#> [29] "Mt_tRNA" "Mt_rRNA"
#> [31] "IG_C_gene" "IG_J_gene"
#> [33] "TR_J_gene" "TR_C_gene"
#> [35] "TR_V_pseudogene" "TR_J_pseudogene"
#> [37] "IG_D_gene" "ribozyme"
#> [39] "IG_C_pseudogene" "TR_D_gene"
#> [41] "IG_J_pseudogene" "scRNA"
#> [43] "scaRNA" "vaultRNA"
#> [45] "sRNA" "macro_lncRNA"
#> [47] "non_coding" "IG_pseudogene"
#> [49] "LRG_gene"
## Update the EnsDb; this is in most instances not necessary at all.
updateEnsDb(EnsDb.Hsapiens.v86)
#> EnsDb for Ensembl:
#> |Backend: SQLite
#> |Db type: EnsDb
#> |Type of Gene ID: Ensembl Gene ID
#> |Supporting package: ensembldb
#> |Db created by: ensembldb package from Bioconductor
#> |script_version: 0.3.0
#> |Creation time: Thu May 18 16:32:27 2017
#> |ensembl_version: 86
#> |ensembl_host: localhost
#> |Organism: homo_sapiens
#> |taxonomy_id: 9606
#> |genome_build: GRCh38
#> |DBSCHEMAVERSION: 2.0
#> | No. of genes: 63970.
#> | No. of transcripts: 216741.
#> |Protein data available.
###### returnFilterColumns
returnFilterColumns(EnsDb.Hsapiens.v86)
#> [1] TRUE
## Get protein coding genes on chromosome X, specifying to return
## only columns gene_name as additional column.
genes(EnsDb.Hsapiens.v86, filter=list(SeqNameFilter("X"),
GeneBiotypeFilter("protein_coding")),
columns=c("gene_name"))
#> GRanges object with 841 ranges and 3 metadata columns:
#> seqnames ranges strand | gene_name
#> <Rle> <IRanges> <Rle> | <character>
#> ENSG00000182378 X 276322-303356 + | PLCXD1
#> ENSG00000178605 X 304529-318819 - | GTPBP6
#> ENSG00000167393 X 333963-386955 - | PPP2R3B
#> ENSG00000185960 X 624344-659411 + | SHOX
#> ENSG00000205755 X 1187549-1212750 - | CRLF2
#> ... ... ... ... . ...
#> ENSG00000277745 X 155459415-155460005 - | H2AFB3
#> ENSG00000185973 X 155490115-155669944 - | TMLHE
#> ENSG00000168939 X 155767812-155782459 + | SPRY3
#> ENSG00000124333 X 155881293-155943769 + | VAMP7
#> ENSG00000124334 X 155997581-156010817 + | IL9R
#> gene_id gene_biotype
#> <character> <character>
#> ENSG00000182378 ENSG00000182378 protein_coding
#> ENSG00000178605 ENSG00000178605 protein_coding
#> ENSG00000167393 ENSG00000167393 protein_coding
#> ENSG00000185960 ENSG00000185960 protein_coding
#> ENSG00000205755 ENSG00000205755 protein_coding
#> ... ... ...
#> ENSG00000277745 ENSG00000277745 protein_coding
#> ENSG00000185973 ENSG00000185973 protein_coding
#> ENSG00000168939 ENSG00000168939 protein_coding
#> ENSG00000124333 ENSG00000124333 protein_coding
#> ENSG00000124334 ENSG00000124334 protein_coding
#> -------
#> seqinfo: 1 sequence from GRCh38 genome
## By default we get also the gene_biotype column as the data was filtered
## on this column.
## This can be changed using the returnFilterColumns option
returnFilterColumns(EnsDb.Hsapiens.v86) <- FALSE
genes(EnsDb.Hsapiens.v86, filter=list(SeqNameFilter("X"),
GeneBiotypeFilter("protein_coding")),
columns=c("gene_name"))
#> GRanges object with 841 ranges and 2 metadata columns:
#> seqnames ranges strand | gene_name
#> <Rle> <IRanges> <Rle> | <character>
#> ENSG00000182378 X 276322-303356 + | PLCXD1
#> ENSG00000178605 X 304529-318819 - | GTPBP6
#> ENSG00000167393 X 333963-386955 - | PPP2R3B
#> ENSG00000185960 X 624344-659411 + | SHOX
#> ENSG00000205755 X 1187549-1212750 - | CRLF2
#> ... ... ... ... . ...
#> ENSG00000277745 X 155459415-155460005 - | H2AFB3
#> ENSG00000185973 X 155490115-155669944 - | TMLHE
#> ENSG00000168939 X 155767812-155782459 + | SPRY3
#> ENSG00000124333 X 155881293-155943769 + | VAMP7
#> ENSG00000124334 X 155997581-156010817 + | IL9R
#> gene_id
#> <character>
#> ENSG00000182378 ENSG00000182378
#> ENSG00000178605 ENSG00000178605
#> ENSG00000167393 ENSG00000167393
#> ENSG00000185960 ENSG00000185960
#> ENSG00000205755 ENSG00000205755
#> ... ...
#> ENSG00000277745 ENSG00000277745
#> ENSG00000185973 ENSG00000185973
#> ENSG00000168939 ENSG00000168939
#> ENSG00000124333 ENSG00000124333
#> ENSG00000124334 ENSG00000124334
#> -------
#> seqinfo: 1 sequence from GRCh38 genome