inst/doc/lefser.R

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

## ----style, echo = FALSE, results = 'asis'------------------------------------
knitr::opts_chunk$set(fig.align = "center")

## ---- eval = FALSE------------------------------------------------------------
#  if (!requireNamespace("BiocManager", quietly = TRUE))
#      install.packages("BiocManager")
#  BiocManager::install("lefser")

## ----include=TRUE,results="hide",message=FALSE,warning=FALSE------------------
library(lefser)

## -----------------------------------------------------------------------------
data(zeller14)
zeller14 <- zeller14[, zeller14$study_condition != "adenoma"]

## -----------------------------------------------------------------------------
table(zeller14$study_condition)

## -----------------------------------------------------------------------------
table(zeller14$age_category)

## -----------------------------------------------------------------------------
table(zeller14$age_category, zeller14$study_condition)

## -----------------------------------------------------------------------------
res <- lefser(zeller14, groupCol = "study_condition", blockCol = "age_category")
head(res)

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lefserPlot(res)

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sessionInfo()