stephenturner / annotables

R data package for annotating/converting Gene IDs
http://www.gettinggeneticsdone.blogspot.com/2015/11/annotables-convert-gene-ids.html
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Use https in host, fix GRCh37 vs 38 #23

Closed stephenturner closed 1 year ago

stephenturner commented 1 year ago

Fixes #22 thanks @joseale2310

Reinstall v0.2.0 to get this fixed. Issue was that at some point during the last round of updates biomart stopped using http. Adding an explicit https to the host in the recipe, and regenerating the data with these updated recipes calling the host explicitly solves the issue.

cc @khughitt @mdozmorov @aaronwolen @mjsteinbaugh

annotables::grch37
#> # A tibble: 66,978 × 9
#>    ensgene         entrez symbol   chr       start    end strand biotype descr…¹
#>    <chr>            <int> <chr>    <chr>     <int>  <int>  <int> <chr>   <chr>  
#>  1 ENSG00000000003   7105 TSPAN6   X      99883667 9.99e7     -1 protei… tetras…
#>  2 ENSG00000000005  64102 TNMD     X      99839799 9.99e7      1 protei… tenomo…
#>  3 ENSG00000000419   8813 DPM1     20     49551404 4.96e7     -1 protei… dolich…
#>  4 ENSG00000000457  57147 SCYL3    1     169818772 1.70e8     -1 protei… SCY1-l…
#>  5 ENSG00000000460  55732 C1orf112 1     169631245 1.70e8      1 protei… chromo…
#>  6 ENSG00000000938   2268 FGR      1      27938575 2.80e7     -1 protei… feline…
#>  7 ENSG00000000971   3075 CFH      1     196621008 1.97e8      1 protei… comple…
#>  8 ENSG00000001036   2519 FUCA2    6     143815948 1.44e8     -1 protei… fucosi…
#>  9 ENSG00000001084   2729 GCLC     6      53362139 5.35e7     -1 protei… glutam…
#> 10 ENSG00000001167   4800 NFYA     6      41040684 4.11e7      1 protei… nuclea…
#> # … with 66,968 more rows, and abbreviated variable name ¹​description
annotables::grch38
#> # A tibble: 75,118 × 9
#>    ensgene         entrez symbol   chr       start    end strand biotype descr…¹
#>    <chr>            <int> <chr>    <chr>     <int>  <int>  <int> <chr>   <chr>  
#>  1 ENSG00000000003   7105 TSPAN6   X     100627108 1.01e8     -1 protei… tetras…
#>  2 ENSG00000000005  64102 TNMD     X     100584936 1.01e8      1 protei… tenomo…
#>  3 ENSG00000000419   8813 DPM1     20     50934867 5.10e7     -1 protei… dolich…
#>  4 ENSG00000000457  57147 SCYL3    1     169849631 1.70e8     -1 protei… SCY1 l…
#>  5 ENSG00000000460  55732 C1orf112 1     169662007 1.70e8      1 protei… chromo…
#>  6 ENSG00000000938   2268 FGR      1      27612064 2.76e7     -1 protei… FGR pr…
#>  7 ENSG00000000971   3075 CFH      1     196651754 1.97e8      1 protei… comple…
#>  8 ENSG00000001036   2519 FUCA2    6     143494812 1.44e8     -1 protei… alpha-…
#>  9 ENSG00000001084   2729 GCLC     6      53497341 5.36e7     -1 protei… glutam…
#> 10 ENSG00000001167   4800 NFYA     6      41072974 4.11e7      1 protei… nuclea…
#> # … with 75,108 more rows, and abbreviated variable name ¹​description
packageVersion("annotables")
#> [1] '0.2.0'

Created on 2023-02-21 with reprex v2.0.2