Some functions require gene models, which can obtained from any source. This function allows you to retrieve a few common built-in ones.
getGeneModels(refAssembly)A string identifier for the reference assembly
A list containing the gene models corresponding to a specific reference assembly.
getGeneModels("hg19")
#> $genesGR
#> GRanges object with 18777 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] chr1 69091-70008 +
#> [2] chr1 367640-368634 +
#> [3] chr1 818043-819983 +
#> [4] chr1 860260-879955 +
#> [5] chr1 895967-901095 +
#> ... ... ... ...
#> [18773] chrY 25275502-25345241 -
#> [18774] chrY 26191376-26194166 -
#> [18775] chrY 26909216-26959626 -
#> [18776] chrY 27177048-27208695 -
#> [18777] chrY 28111776-28114889 -
#> -------
#> seqinfo: 25 sequences from GRCh37 genome
#>
#> $exonsGR
#> GRanges object with 234018 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] chr1 69091-70008 +
#> [2] chr1 367640-368634 +
#> [3] chr1 818043-818058 +
#> [4] chr1 819496-819513 +
#> [5] chr1 819961-819983 +
#> ... ... ... ...
#> [234014] chrY 27198298-27198366 -
#> [234015] chrY 27208540-27208695 -
#> [234016] chrY 28111776-28111809 -
#> [234017] chrY 28111970-28111984 -
#> [234018] chrY 28114876-28114889 -
#> -------
#> seqinfo: 25 sequences from GRCh37 genome
#>
#> $threeUTRGR
#> GRanges object with 66470 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] chr7 299947-300711 +
#> [2] chr7 825291-826112 +
#> [3] chr7 883274-883509 +
#> [4] chr7 912969-914557 +
#> [5] chr7 926277-926287 +
#> ... ... ... ...
#> [66466] chr21 47720095-47720150 -
#> [66467] chr21 47720268-47720708 -
#> [66468] chr21 47721044-47721912 -
#> [66469] chr21 47734785-47734870 -
#> [66470] chr21 48018875-48019363 -
#> -------
#> seqinfo: 24 sequences from GRCh37 genome
#>
#> $fiveUTRGR
#> GRanges object with 58570 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] chr7 192969-193199 +
#> [2] chr7 766338-766357 +
#> [3] chr7 808112-808784 +
#> [4] chr7 856252-856310 +
#> [5] chr7 856392-856547 +
#> ... ... ... ...
#> [58566] chr21 47737926-47739051 -
#> [58567] chr21 47740551-47740739 -
#> [58568] chr21 47742553-47743789 -
#> [58569] chr21 48022329-48022806 -
#> [58570] chr21 48024926-48025121 -
#> -------
#> seqinfo: 24 sequences from GRCh37 genome
#>