Create a GTFParquet object
Examples
gtf <- GTFParquet(system.file("gc49", package="lkparq"))
genes(gtf)
#> GRanges object with 78691 ranges and 6 metadata columns:
#> seqnames ranges strand | gene_name
#> <Rle> <IRanges> <Rle> | <character>
#> ENSG00000290825 chr1 11121-24894 + | DDX11L16
#> ENSG00000223972 chr1 12010-13670 + | DDX11L1
#> ENSG00000310526 chr1 14356-30744 - | WASH7P
#> ENSG00000227232 chr1 14696-24886 - | WASH7P
#> ENSG00000278267 chr1 17369-17436 - | MIR6859-1
#> ... ... ... ... . ...
#> ENSG00000292369 chrY 57190738-57208756 + | ENSG00000292369
#> ENSG00000292370 chrY 57201135-57203405 - | WASIR1
#> ENSG00000292372 chrY 57207346-57212230 + | WASH6P
#> ENSG00000310542 chrY 57208516-57215634 - | ENSG00000310542
#> ENSG00000292371 chrY 57212184-57214397 - | DDX11L16
#> gene_type source level
#> <character> <character> <integer>
#> ENSG00000290825 lncRNA HAVANA <NA>
#> ENSG00000223972 transcribed_unproces.. HAVANA <NA>
#> ENSG00000310526 lncRNA HAVANA <NA>
#> ENSG00000227232 transcribed_unproces.. HAVANA <NA>
#> ENSG00000278267 miRNA ENSEMBL <NA>
#> ... ... ... ...
#> ENSG00000292369 lncRNA HAVANA <NA>
#> ENSG00000292370 lncRNA HAVANA <NA>
#> ENSG00000292372 protein_coding HAVANA <NA>
#> ENSG00000310542 lncRNA HAVANA <NA>
#> ENSG00000292371 unprocessed_pseudogene HAVANA <NA>
#> tags havana_gene
#> <character> <character>
#> ENSG00000290825 overlaps_pseudogene <NA>
#> ENSG00000223972 <NA> OTTHUMG00000000961.2
#> ENSG00000310526 ncRNA_host;overlappi.. <NA>
#> ENSG00000227232 overlapping_locus OTTHUMG00000000958.1
#> ENSG00000278267 <NA> <NA>
#> ... ... ...
#> ENSG00000292369 overlapping_locus OTTHUMG00000184987.2
#> ENSG00000292370 <NA> OTTHUMG00000022676.3
#> ENSG00000292372 overlapping_locus OTTHUMG00000022677.5
#> ENSG00000310542 overlapping_locus;ov.. <NA>
#> ENSG00000292371 <NA> OTTHUMG00000022678.1
#> -------
#> seqinfo: 25 sequences from GRCh38 genome; no seqlengths
genes(gtf, filter = list(gene_type = "protein_coding"))
#> GRanges object with 20097 ranges and 6 metadata columns:
#> seqnames ranges strand | gene_name
#> <Rle> <IRanges> <Rle> | <character>
#> ENSG00000186092 chr1 65419-71585 + | OR4F5
#> ENSG00000284733 chr1 450740-451678 - | OR4F29
#> ENSG00000284662 chr1 685716-686654 - | OR4F16
#> ENSG00000187634 chr1 923923-944575 + | SAMD11
#> ENSG00000188976 chr1 943527-960714 - | NOC2L
#> ... ... ... ... . ...
#> ENSG00000185894 chrY 25030901-25062548 - | BPY2C
#> ENSG00000172288 chrY 25622117-25624902 + | CDY1
#> ENSG00000292366 chrY 57067747-57130289 + | VAMP7
#> ENSG00000292373 chrY 57184216-57199537 + | IL9R
#> ENSG00000292372 chrY 57207346-57212230 + | WASH6P
#> gene_type source level tags
#> <character> <character> <integer> <character>
#> ENSG00000186092 protein_coding HAVANA <NA> <NA>
#> ENSG00000284733 protein_coding HAVANA <NA> <NA>
#> ENSG00000284662 protein_coding HAVANA <NA> <NA>
#> ENSG00000187634 protein_coding HAVANA <NA> <NA>
#> ENSG00000188976 protein_coding HAVANA <NA> <NA>
#> ... ... ... ... ...
#> ENSG00000185894 protein_coding HAVANA <NA> <NA>
#> ENSG00000172288 protein_coding HAVANA <NA> retrogene
#> ENSG00000292366 protein_coding HAVANA <NA> <NA>
#> ENSG00000292373 protein_coding HAVANA <NA> overlapping_locus
#> ENSG00000292372 protein_coding HAVANA <NA> overlapping_locus
#> havana_gene
#> <character>
#> ENSG00000186092 OTTHUMG00000001094.4
#> ENSG00000284733 OTTHUMG00000002860.3
#> ENSG00000284662 OTTHUMG00000002581.3
#> ENSG00000187634 OTTHUMG00000040719.11
#> ENSG00000188976 OTTHUMG00000040720.2
#> ... ...
#> ENSG00000185894 OTTHUMG00000045199.3
#> ENSG00000172288 OTTHUMG00000045274.2
#> ENSG00000292366 OTTHUMG00000022679.3
#> ENSG00000292373 OTTHUMG00000022720.1
#> ENSG00000292372 OTTHUMG00000022677.5
#> -------
#> seqinfo: 25 sequences from GRCh38 genome; no seqlengths