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waldronlab
Update script to generate example data (Zeller14)
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
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#> ctype en_US.UTF-8
#> tz America/New_York
#> date 2024-09-04
#> pandoc 3.1.12.3 @ /usr/bin/ (via rmarkdown)
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#>
#> [1] /home/user/R/x86_64-pc-linux-gnu-library/4.4
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#>
#> ──────────────────────────────────────────────────────────────────────────────
Created on 2024-09-04 with reprex v2.1.1
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.
