Get all the files in GTEx dataset for Download page
Details
The returned tibble includes a nested list column, "filesets". This details files, sub-categorised by fileset (see examples section).
See also
Other Datasets Endpoints:
get_annotation(),
get_collapsed_gene_model_exon(),
get_downloads_page_data(),
get_full_get_collapsed_gene_model_exon(),
get_functional_annotation(),
get_linkage_disequilibrium_by_variant_data(),
get_linkage_disequilibrium_data(),
get_sample_datasets_endpoints(),
get_subject(),
get_tissue_site_detail(),
get_variant(),
get_variant_by_location()
Examples
# \dontrun{
# Column "filesets" is a list column
get_file_list()
#> # A tibble: 11 × 10
#> name subpath dbgapId dataset release order type id description
#> <chr> <chr> <chr> <chr> <chr> <int> <chr> <chr> <chr>
#> 1 GTEx Analysis … gtex_a… "phs00… GTEx v3 10 data… gtex… ""
#> 2 GTEx Analysis … gtex_a… "" GTEx v6p 7 data… gtex… "The GTEx …
#> 3 Biobank Invent… gtex_b… "" GTEx biobank 5 data… biob… ""
#> 4 GTEx Analysis … gtex_a… "phs00… GTEx v7 6 data… gtex… ""
#> 5 GTEx Analysis … gtex_a… "phs00… GTEx v6 8 data… gtex… ""
#> 6 Additional Dat… gtex_a… "" GTEx additi… 3 data… addi… ""
#> 7 GTEx Analysis … gtex_a… "phs00… GTEx v4 9 data… gtex… ""
#> 8 External Datas… gtex_e… "" GTEx extern… 4 data… exte… ""
#> 9 GTEx Analysis … gtex_a… "phs00… GTEx v8 1 data… gtex… "The GTEx …
#> 10 eGTEx gtex_e… "" GTEx egtex 2 data… egtex "The Enhan…
#> 11 GTEx Analysis … gtex_a… "phs00… GTEx v9 0 data… gtex… "Open-acce…
#> # ℹ 1 more variable: filesets <list>
# Get "GTEx Analysis V9" file list
gtex_v9_files <- get_file_list() |>
dplyr::filter(name == "GTEx Analysis V9") |>
dplyr::pull(filesets)
# "GTEx Analysis V9" filesets
names(gtex_v9_files[[1]])
#> [1] "snRNA-Seq Data" "Long Read Data"
# "GTEx Analysis V9", "snRNA-Seq Data" fileset files
names(gtex_v9_files[[1]][["snRNA-Seq Data"]]$files)
#> [1] "GTEx_8_tissues_snRNAseq_atlas_071421.public_obs.h5ad"
#> [2] "GTEx_8_tissues_snRNAseq_immune_atlas_071421.public_obs.h5ad"
# }