Unable to import the example GWAS summary statistics when MUNGE = FALSE #136
Description
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