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)

Arguments

refAssembly

A string identifier for the reference assembly

Value

A list containing the gene models corresponding to a specific reference assembly.

Examples

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
#>