vignettes/downloadR.Rmd
downloadR.RmdGeneric function for downloading files with a variety of methods, including multi-threaded downloading of a single file with axel.
rda_url <- "https://github.com/RajLabMSSM/echolocatoR/raw/master/data/BST1.rda"
out_path <- downloadR::downloader(input_url = rda_url,
download_method = "axel")## Downloading with axel (using 11 cores).## + CONDA:: Identified axel executable in echoR env.## Time difference of 2.717356 secs
BST1 <- downloadR::load_rdata(out_path)More specialized downloading function for Variant Call Format (VCF) files that downloads both the VCF and its index file (if available).
vcf_url <- "https://gwas.mrcieu.ac.uk/files/ieu-a-298/ieu-a-298.vcf.gz"
out_paths <- downloadR::download_vcf(vcf_url = vcf_url)## Downloading VCF ==> /var/folders/zq/h7mtybc533b1qzkys_ttgpth0000gn/T//RtmpVYiT6M/ieu-a-298.vcf.gz## Downloading with download.file.## Time difference of 0.28791 secs## Downloading VCF index ==> https://gwas.mrcieu.ac.uk/files/ieu-a-298/ieu-a-298.vcf.gz.tbi## Downloading with download.file.## Time difference of 0.2106071 secs
utils::sessionInfo()## R version 4.1.0 (2021-05-18)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur 10.16
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] downloadR_0.99.0 BiocStyle_2.20.2
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.7 bslib_0.2.5.1 compiler_4.1.0
## [4] BiocManager_1.30.16 jquerylib_0.1.4 remotes_2.4.0
## [7] prettyunits_1.1.1 tools_4.1.0 testthat_3.0.4
## [10] digest_0.6.27 pkgbuild_1.2.0 pkgload_1.2.1
## [13] lattice_0.20-44 lifecycle_1.0.0 jsonlite_1.7.2
## [16] evaluate_0.14 memoise_2.0.0 png_0.1-7
## [19] rlang_0.4.11 Matrix_1.3-4 cli_3.0.1
## [22] rstudioapi_0.13 parallel_4.1.0 yaml_2.2.1
## [25] pkgdown_1.6.1 xfun_0.25 fastmap_1.1.0
## [28] echoconda_0.99.0 withr_2.4.2 stringr_1.4.0
## [31] knitr_1.33 desc_1.3.0 fs_1.5.0
## [34] sass_0.4.0 systemfonts_1.0.2 devtools_2.4.2
## [37] grid_4.1.0 rprojroot_2.0.2 reticulate_1.20
## [40] glue_1.4.2 R6_2.5.1 textshaping_0.3.5
## [43] processx_3.5.2 rmarkdown_2.10 bookdown_0.23
## [46] sessioninfo_1.1.1 purrr_0.3.4 callr_3.7.0
## [49] magrittr_2.0.1 usethis_2.0.1 ps_1.6.0
## [52] htmltools_0.5.2 ellipsis_0.3.2 ragg_1.1.3
## [55] stringi_1.7.4 cachem_1.0.6 crayon_1.4.1