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ramiromagno / gwasrapidd

gwasrapidd: an R package to query, download and wrangle GWAS Catalog data
https://rmagno.eu/gwasrapidd/
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"get_variants" query error #6

Closed tzup closed 4 years ago

tzup commented 4 years ago 
library(gwasrapidd)
ae_variants = get_variants(association_id = c("20171" ,   "20172"))

results in error:

Error: 'unnest_legacy' is not an exported object from 'namespace:tidyr'
ramiromagno commented 4 years ago

Hi @tzup :

Thank you for reporting this.

Could you please paste the output of sessionInfo()?

ramiromagno commented 4 years ago

In my environment your query works:

library(gwasrapidd)
ae_variants = get_variants(association_id = c("20171" , "20172"))

#> An object of class "variants"
#> Slot "variants":
#> # A tibble: 2 x 7
#>   variant_id merged functional_class chromosome_name chromosome_posi…
#>   <chr>       <int> <chr>            <chr>                      <int>
#> 1 rs479844        0 regulatory_regi… 11                      65784486
#> 2 rs2164983       0 intergenic_vari… 19                       8679120
#> # … with 2 more variables: chromosome_region <chr>, last_update_date <dttm>
#> 
#> Slot "genomic_contexts":
#> # A tibble: 42 x 12
#>    variant_id gene_name chromosome_name chromosome_posi… distance is_mapped_gene
#>    <chr>      <chr>     <chr>                      <int>    <int> <lgl>         
#>  1 rs479844   EFEMP2    11                      65784486    81955 FALSE         
#>  2 rs479844   SNX32     11                      65784486    49154 FALSE         
#>  3 rs479844   KRT8P26   11                      65784486    56272 FALSE         
#>  4 rs479844   KAT5      11                      65784486    64882 FALSE         
#>  5 rs479844   RNASEH2C  11                      65784486    63539 FALSE         
#>  6 rs479844   CTSW      11                      65784486    95351 FALSE         
#>  7 rs479844   KRT8P26   11                      65784486    56471 FALSE         
#>  8 rs479844   RNASEH2C  11                      65784486    63548 FALSE         
#>  9 rs479844   KAT5      11                      65784486    64882 FALSE         
#> 10 rs479844   OVOL1-AS1 11                      65784486     4565 FALSE         
#> # … with 32 more rows, and 6 more variables: is_closest_gene <lgl>,
#> #   is_intergenic <lgl>, is_upstream <lgl>, is_downstream <lgl>, source <chr>,
#> #   mapping_method <chr>
#> 
#> Slot "ensembl_ids":
#> # A tibble: 23 x 3
#>    variant_id gene_name  ensembl_id     
#>    <chr>      <chr>      <chr>          
#>  1 rs479844   EFEMP2     ENSG00000172638
#>  2 rs479844   SNX32      ENSG00000172803
#>  3 rs479844   KRT8P26    ENSG00000214659
#>  4 rs479844   KAT5       ENSG00000172977
#>  5 rs479844   RNASEH2C   ENSG00000172922
#>  6 rs479844   CTSW       ENSG00000172543
#>  7 rs479844   OVOL1-AS1  ENSG00000255120
#>  8 rs479844   OVOL1      ENSG00000172818
#>  9 rs479844   AP001266.1 ENSG00000255404
#> 10 rs479844   MUS81      ENSG00000172732
#> # … with 13 more rows
#> 
#> Slot "entrez_ids":
#> # A tibble: 19 x 3
#>    variant_id gene_name    entrez_id
#>    <chr>      <chr>        <chr>    
#>  1 rs479844   EFEMP2       30008    
#>  2 rs479844   SNX32        254122   
#>  3 rs479844   KRT8P26      390211   
#>  4 rs479844   KAT5         10524    
#>  5 rs479844   RNASEH2C     84153    
#>  6 rs479844   CTSW         1521     
#>  7 rs479844   OVOL1-AS1    101927828
#>  8 rs479844   OVOL1        5017     
#>  9 rs479844   MUS81        80198    
#> 10 rs479844   CFL1         1072     
#> 11 rs479844   FIBP         9158     
#> 12 rs479844   RN7SL309P    106481007
#> 13 rs479844   AP5B1        91056    
#> 14 rs2164983  ACTL9        284382   
#> 15 rs2164983  OR2Z1        284383   
#> 16 rs2164983  RPL23AP78    100271624
#> 17 rs2164983  ADAMTS10     81794    
#> 18 rs2164983  LINC01862    105372267
#> 19 rs2164983  LOC107983991 107983991
ramiromagno commented 4 years ago

@tzup: can you please check if your version of the package tidyr is lower than 0.8.3.9000?

tzup commented 4 years ago

Hi Ramiro,

No worry. It turns out that I did not keep my libraries up to date.

Thank you for getting back to me 😊

Tzu Lip Phang PH.D Associate Professor of Bioinformatics Director, Translational Informatics Computational Resources (TICR) Colorado Center for Personalized Medicine (CCPM) University of Colorado, Department of Medicine Office: Building 500 5th Floor East Wing Q20-E5324 Phone: 303-724-6057

From: Ramiro Magno notifications@github.com Reply-To: ramiromagno/gwasrapidd reply@reply.github.com Date: Tuesday, February 18, 2020 at 6:48 PM To: ramiromagno/gwasrapidd gwasrapidd@noreply.github.com Cc: "Phang, Tzu" TZU.PHANG@CUANSCHUTZ.EDU, Mention mention@noreply.github.com Subject: Re: [ramiromagno/gwasrapidd] "get_variants" query error (#6)

@tzuphttps://github.com/tzup: can you please check if your version of the package tidyr is lower than 0.8.3.9000?

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ramiromagno commented 4 years ago

My pleasure. Don't hesitate to contact me if you need further help.