construct_lefse_table: construct_lefse_table

Description Usage Arguments Examples

View source: R/construct_lefse_table.R

Description

construct_lefse_table can construct a LEfSe-format OTU table. See http://huttenhower.sph.harvard.edu/galaxy/ -> LEfSe -> Format Data for LEfSe for more details.

Usage

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construct_lefse_table(phyloseq, feature, level = "all")

Arguments

phyloseq

A phyloseq object contain otu table, taxonomy table, sample metadata and phylogenetic tree.

feature

The column name of the feature you want to select. In final table, feature will be the first row.

level

The coloumn name of the taxonomy level to select. Default is "all". If "all" then retain all taxonomy level, else retain the taxonomy from Kingdom to selected level, drop everything else. Level name should be one of c("all", "Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species"). Taxonomy will be seperated by "|".

Examples

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# minimum usage
construct_lefse_table(demo_phyloseq_object, feature = "diagnosis") %>%
  .[1:20,1:5]

yeguanhuav/visual16S documentation built on Aug. 11, 2019, 8:51 a.m.