Update script to generate example data (Zeller14) #58
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Yeah, this script doesn't work anymore with the current version of the curatedMetagenomicData package. I remember it's not just the script-level issue; the exposed data has changed. |
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I think the code in https://github.com/waldronlab/lefser/blob/devel/inst/scripts/zeller14.R should be updated with a newer version of curatedMetagenomicData:
suppressMessages({ library(curatedMetagenomicData) }) exampledata <- curatedMetagenomicData("ZellerG_2014.metaphlan_bugs_list.stool", counts = TRUE, dryrun = FALSE)[[1]] #> Error: no resources available in curatedMetagenomicData curatedMetagenomicData("ZellerG_2014") #> 2021-03-31.ZellerG_2014.gene_families #> 2021-03-31.ZellerG_2014.marker_abundance #> 2021-03-31.ZellerG_2014.marker_presence #> 2021-03-31.ZellerG_2014.pathway_abundance #> 2021-03-31.ZellerG_2014.pathway_coverage #> 2021-03-31.ZellerG_2014.relative_abundance sessioninfo::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.4.0 (2024-04-24) #> os Pop!_OS 22.04 LTS #> system x86_64, linux-gnu #> ui X11 #> language (EN) #> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz America/New_York #> date 2024-09-04 #> pandoc 3.1.12.3 @ /usr/bin/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> 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