Unable to import the example GWAS summary statistics when MUNGE = FALSE

[Sheenlei]

1. Bug description

I'm trying to import example GWAS summary statistics using the following code:

gwas_sumstats_path <- MAGMA.Celltyping::get_example_gwas(
  trait = "fluid_intelligence", 
  munged = FALSE
  )

Console output

Downloading example GWAS: fluid_intelligence
trying URL 'https://www.dropbox.com/s/t3lrfj1id8133sx/20016_irnt.gwas.imputed_v3.both_sexes.tsv.bgz?dl=1'
Error in utils::download.file(url = URL, destfile = gwas_sumstats_path) : 
  cannot open URL 'https://www.dropbox.com/s/t3lrfj1id8133sx/20016_irnt.gwas.imputed_v3.both_sexes.tsv.bgz?dl=1'
In addition: Warning message:
In utils::download.file(url = URL, destfile = gwas_sumstats_path) :
  cannot open URL 'https://www.dropbox.com/s/dl/t3lrfj1id8133sx/20016_irnt.gwas.imputed_v3.both_sexes.tsv.bgz': HTTP status was '404 Not Found'

When I do MUNGE = TRUE, it works to import the munged GWAS summary statistics. I guess there may be some problem while downloading the pre-munged GWAS.

3. Session info

R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] SNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.20 BSgenome_1.64.0                         
 [3] rtracklayer_1.56.1                       Biostrings_2.64.1                       
 [5] XVector_0.36.0                           GenomicRanges_1.48.0                    
 [7] GenomeInfoDb_1.32.4                      IRanges_2.30.1                          
 [9] S4Vectors_0.34.0                         BiocGenerics_0.42.0                     
[11] dplyr_1.0.10                             MAGMA.Celltyping_2.0.7                  

loaded via a namespace (and not attached):
  [1] backports_1.4.1               AnnotationHub_3.4.0           BiocFileCache_2.4.0          
  [4] plyr_1.8.8                    googleAuthR_2.0.0             lazyeval_0.2.2               
  [7] splines_4.2.1                 orthogene_1.2.1               ewceData_1.4.0               
 [10] BiocParallel_1.30.4           ggplot2_3.4.0                 digest_0.6.30                
 [13] yulab.utils_0.0.5             htmltools_0.5.3               RNOmni_1.0.1                 
 [16] fansi_1.0.3                   magrittr_2.0.3                memoise_2.0.1                
 [19] limma_3.52.4                  matrixStats_0.62.0            R.utils_2.12.2               
 [22] timechange_0.1.1              prettyunits_1.1.1             colorspace_2.0-3             
 [25] blob_1.2.3                    rappdirs_0.3.3                gitcreds_0.1.2               
 [28] xfun_0.35                     crayon_1.5.2                  RCurl_1.98-1.9               
 [31] jsonlite_1.8.3                lme4_1.1-31                   VariantAnnotation_1.42.1     
 [34] ape_5.6-2                     glue_1.6.2                    gtable_0.3.1                 
 [37] gargle_1.2.1                  zlibbioc_1.42.0               HGNChelper_0.8.1             
 [40] DelayedArray_0.22.0           car_3.1-1                     SingleCellExperiment_1.18.1  
 [43] abind_1.4-5                   scales_1.2.1                  DBI_1.1.3                    
 [46] rstatix_0.7.1                 Rcpp_1.0.9                    viridisLite_0.4.1            
 [49] xtable_1.8-4                  progress_1.2.2                gridGraphics_0.5-1           
 [52] tidytree_0.4.1                bit_4.0.5                     htmlwidgets_1.5.4            
 [55] httr_1.4.4                    ellipsis_0.3.2                pkgconfig_2.0.3              
 [58] XML_3.99-0.12                 R.methodsS3_1.8.2             dbplyr_2.2.1                 
 [61] utf8_1.2.2                    ggplotify_0.1.0               tidyselect_1.2.0             
 [64] rlang_1.0.6                   reshape2_1.4.4                later_1.3.0                  
 [67] AnnotationDbi_1.58.0          munsell_0.5.0                 BiocVersion_3.15.2           
 [70] tools_4.2.1                   cachem_1.0.6                  cli_3.4.1                    
 [73] generics_0.1.3                RSQLite_2.2.18                ExperimentHub_2.4.0          
 [76] MungeSumstats_1.4.5           broom_1.0.1                   evaluate_0.18                
 [79] ggdendro_0.1.23               stringr_1.4.1                 fastmap_1.1.0                
 [82] yaml_2.3.6                    ggtree_3.4.4                  knitr_1.40                   
 [85] babelgene_22.9                bit64_4.0.5                   fs_1.5.2                     
 [88] purrr_0.3.5                   gh_1.3.1                      KEGGREST_1.36.3              
 [91] gprofiler2_0.2.1              nlme_3.1-160                  mime_0.12                    
 [94] R.oo_1.25.0                   aplot_0.1.8                   xml2_1.3.3                   
 [97] biomaRt_2.52.0                compiler_4.2.1                rstudioapi_0.14              
[100] plotly_4.10.1                 filelock_1.0.2                curl_4.3.3                   
[103] png_0.1-7                     interactiveDisplayBase_1.34.0 ggsignif_0.6.4               
[106] treeio_1.20.2                 tibble_3.1.8                  EWCE_1.4.0                   
[109] homologene_1.4.68.19.3.27     stringi_1.7.8                 GenomicFeatures_1.48.4       
[112] lattice_0.20-45               Matrix_1.5-3                  nloptr_2.0.3                 
[115] vctrs_0.5.1                   pillar_1.8.1                  lifecycle_1.0.3              
[118] BiocManager_1.30.19           cowplot_1.1.1                 data.table_1.14.6            
[121] bitops_1.0-7                  httpuv_1.6.6                  patchwork_1.1.2              
[124] R6_2.5.1                      BiocIO_1.6.0                  promises_1.2.0.1             
[127] gridExtra_2.3                 codetools_0.2-18              boot_1.3-28                  
[130] MASS_7.3-58.1                 assertthat_0.2.1              SummarizedExperiment_1.26.1  
[133] rjson_0.2.21                  GenomicAlignments_1.32.1      Rsamtools_2.12.0             
[136] GenomeInfoDbData_1.2.8        parallel_4.2.1                hms_1.1.2                    
[139] grid_4.2.1                    ggfun_0.0.8                   minqa_1.2.5                  
[142] tidyr_1.2.1                   rmarkdown_2.18                MatrixGenerics_1.8.1         
[145] carData_3.0-5                 ggpubr_0.5.0                  piggyback_0.1.4              
[148] lubridate_1.9.0               Biobase_2.56.0                shiny_1.7.3                  
[151] restfulr_0.0.15              

[bschilder]

Seems the link has been disabled by dropbox.

I'll implement an alternative