search

ropensci / UCSCXenaTools

:package: An R package for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq https://cran.r-project.org/web/packages/UCSCXenaTools/
https://docs.ropensci.org/UCSCXenaTools
GNU General Public License v3.0
106 stars 12 forks source link

Enhancements #42

Open ShixiangWang opened 3 months ago

ShixiangWang commented 3 months ago
  1. fetch_dataset_samples(host, dataset) failed in query all samples

Don't know why

> fetch_dataset_samples(host, dataset)
Error in FUN(X[[i]], ...) : is.atomic(p) | is.list(p) is not TRUE

Change to fetch_dataset_samples(host, dataset, -1) works

  1. Use the new query to hance the data query pipeline?

https://github.com/ropensci/UCSCXenaTools/commit/19f2cad196831a53becdb5fad538ba72e9755662

ShixiangWang commented 2 months ago

影响了服务器部署的 shiny

Browse[1]> host = "https://icgc.xenahubs.net"
Browse[1]> dataset = "sp/copy_number_somatic_mutation.all_projects.specimen"
Browse[1]> fetch_dataset_samples(host, dataset)
Error in FUN(X[[i]], ...) : is.atomic(p) | is.list(p) is not TRUE
Browse[1]> fetch_dataset_samples(host, dataset, -1) |> head()
[1] "SP29019" "SP29013" "SP49531" "SP49536" "SP51922" "SP51932"
Browse[1]> fetch_dataset_samples(host, dataset, -1) |> length()
[1] 20530