inst/scripts/zeller14.R

In lefser: R implementation of the LEfSE method for microbiome biomarker discovery

## code to prepare example dataset goes here
## can change dataset by replacing ZellerG_2014 with any other dataset

library(curatedMetagenomicData)
library(SummarizedExperiment)
exampledata <-
  curatedMetagenomicData("ZellerG_2014.metaphlan_bugs_list.stool",
                         counts = TRUE,
                         dryrun = FALSE)[[1]]
zeller14 <- as(exampledata, "SummarizedExperiment")
colData(zeller14) <- colData(zeller14)[, c(4,8)]
usethis::use_data(zeller14, overwrite = TRUE)