get_exons.RdGet all exons as GRanges object
get_exons(edb, columns = c("tx_id", "gene_id", "symbol", "gene_name"), ...)An Ensbel database object (EnsDb for Ensembl), e.g. from EnsDb.Hsapiens.v75
Annotation columns. See ensembldb::exons()
Additional paramters passed to ensembldb::exons()
A GenomicRanges::GRanges() object with regions.
require(EnsDb.Hsapiens.v75)
#> Loading required package: EnsDb.Hsapiens.v75
#> Loading required package: ensembldb
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#> Loading required package: GenomicRanges
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#> The following object is masked from ‘package:utils’:
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#> Loading required package: IRanges
#> Loading required package: GenomeInfoDb
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#> Loading required package: AnnotationFilter
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#> The following object is masked from 'package:stats':
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#> filter
edb <- EnsDb.Hsapiens.v75
get_exons(edb)
#> Warning: cannot switch some GRCh37's seqlevels from NCBI to UCSC style
#> GRanges object with 1314240 ranges and 5 metadata columns:
#> seqnames ranges strand | tx_id
#> <Rle> <IRanges> <Rle> | <character>
#> ENSE00002234944 chr1 11869-12227 + | ENST00000456328
#> ENSE00002234632 chr1 11872-12227 + | ENST00000515242
#> ENSE00002269724 chr1 11874-12227 + | ENST00000518655
#> ENSE00001948541 chr1 12010-12057 + | ENST00000450305
#> ENSE00001671638 chr1 12179-12227 + | ENST00000450305
#> ... ... ... ... . ...
#> ENSE00001741452 chrY 28774418-28774584 - | ENST00000435945
#> ENSE00001681574 chrY 28776794-28776896 - | ENST00000435945
#> ENSE00001638296 chrY 28779492-28779578 - | ENST00000435945
#> ENSE00001797328 chrY 28780670-28780799 - | ENST00000435945
#> ENSE00001794473 chrY 59001391-59001635 + | ENST00000431853
#> gene_id symbol gene_name exon_id
#> <character> <character> <character> <character>
#> ENSE00002234944 ENSG00000223972 DDX11L1 DDX11L1 ENSE00002234944
#> ENSE00002234632 ENSG00000223972 DDX11L1 DDX11L1 ENSE00002234632
#> ENSE00002269724 ENSG00000223972 DDX11L1 DDX11L1 ENSE00002269724
#> ENSE00001948541 ENSG00000223972 DDX11L1 DDX11L1 ENSE00001948541
#> ENSE00001671638 ENSG00000223972 DDX11L1 DDX11L1 ENSE00001671638
#> ... ... ... ... ...
#> ENSE00001741452 ENSG00000237917 PARP4P1 PARP4P1 ENSE00001741452
#> ENSE00001681574 ENSG00000237917 PARP4P1 PARP4P1 ENSE00001681574
#> ENSE00001638296 ENSG00000237917 PARP4P1 PARP4P1 ENSE00001638296
#> ENSE00001797328 ENSG00000237917 PARP4P1 PARP4P1 ENSE00001797328
#> ENSE00001794473 ENSG00000235857 CTBP2P1 CTBP2P1 ENSE00001794473
#> -------
#> seqinfo: 273 sequences (1 circular) from 2 genomes (hg19, GRCh37)
# get exons for specifc genes:
get_exons(edb, filter = SymbolFilter(c("TP53", "BRAF")))
#> GRanges object with 178 ranges and 5 metadata columns:
#> seqnames ranges strand | tx_id
#> <Rle> <IRanges> <Rle> | <character>
#> ENSE00001657961 chr17 7565097-7565332 - | ENST00000413465
#> ENSE00002204316 chr17 7569404-7569562 - | ENST00000359597
#> ENSE00003492844 chr17 7571720-7573008 - | ENST00000504290
#> ENSE00003492844 chr17 7571720-7573008 - | ENST00000510385
#> ENSE00003492844 chr17 7571720-7573008 - | ENST00000504937
#> ... ... ... ... . ...
#> ENSE00003603715 chr7 140549911-140550012 - | ENST00000497784
#> ENSE00003470674 chr7 140549911-140550012 - | ENST00000469930
#> ENSE00001154485 chr7 140624366-140624564 - | ENST00000288602
#> ENSE00001862791 chr7 140624366-140624458 - | ENST00000497784
#> ENSE00001888191 chr7 140624366-140624509 - | ENST00000469930
#> gene_id symbol gene_name exon_id
#> <character> <character> <character> <character>
#> ENSE00001657961 ENSG00000141510 TP53 TP53 ENSE00001657961
#> ENSE00002204316 ENSG00000141510 TP53 TP53 ENSE00002204316
#> ENSE00003492844 ENSG00000141510 TP53 TP53 ENSE00003492844
#> ENSE00003492844 ENSG00000141510 TP53 TP53 ENSE00003492844
#> ENSE00003492844 ENSG00000141510 TP53 TP53 ENSE00003492844
#> ... ... ... ... ...
#> ENSE00003603715 ENSG00000157764 BRAF BRAF ENSE00003603715
#> ENSE00003470674 ENSG00000157764 BRAF BRAF ENSE00003470674
#> ENSE00001154485 ENSG00000157764 BRAF BRAF ENSE00001154485
#> ENSE00001862791 ENSG00000157764 BRAF BRAF ENSE00001862791
#> ENSE00001888191 ENSG00000157764 BRAF BRAF ENSE00001888191
#> -------
#> seqinfo: 2 sequences from hg19 genome