lefserClades: Run lefser at different clades

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

Run lefser at different clades

Description

lefesrCaldes Agglomerates the features abundance at different taxonomic ranks using mia::splitByRanks and performs lefser at each rank. The analysis is run at the species, genus, family, order, class, and phylum levels.

Usage

lefserClades(relab, ...)

Arguments

relab	A (Tree) SummarizedExperiment with full taxonomy in the rowData.
...	Arguments passed to the lefser function.

Details

When running lefserClades, all features with NAs in the rowData will be dropped. This is to avoid creating artificial clades with NAs.

Value

An object of class 'lefser_df_clades', "lefser_df", and 'data.frame'.

Examples

data("zeller14")
z14 <- zeller14[, zeller14$study_condition != "adenoma"]
tn <- get_terminal_nodes(rownames(z14))
z14tn <- z14[tn, ]
z14tn_ra <- relativeAb(z14tn)
z14_input <- rowNames2RowData(z14tn_ra)

resCl <- lefserClades(relab = z14_input, classCol = "study_condition")

waldronlab/lefser documentation built on Oct. 17, 2024, 11:44 a.m.