lefser on pathway abundances using ZellerG_2014 from cMD

lefser_pathwayab.R

suppressPackageStartupMessages({
  library(lefser)
  library(curatedMetagenomicData)
})
zeller <-
  curatedMetagenomicData("ZellerG_2014.pathway_abundance",
                         counts = TRUE,
                         dryrun = FALSE)[[1]]
zeller <- zeller[, zeller$study_condition != "adenoma"]
zeller <- relativeAb(zeller)

lefse_results1 <-
  lefser(
    zeller,
    groupCol = "study_condition",
    kruskal.threshold = 0.05,
    lda.threshold = 2
  )
head(lefse_results1)

lefse_results2 <-
  lefser(
    zeller,
    groupCol = "study_condition",
    kruskal.threshold = 1e-6,
    lda.threshold = 2
  )
head(lefse_results2)

lefse_results3 <-
  lefser(
    zeller,
    groupCol = "study_condition",
    kruskal.threshold = 0.05,
    lda.threshold = 2000
head(lefse_results3)