construct_lefse_table: construct_lefse_table

In yeguanhuav/visualization416S: Visualization functions for 16S and Metagenomics analysis

construct_lefse_table

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

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

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

yeguanhuav/visualization416S documentation built on March 22, 2022, 9:03 p.m.