ezstat {mbX} | R Documentation |
Statistical Analysis and Visualization of Microbiome Data
Description
Performs Kruskal_Wallis tests, post_hoc Dunn comparisons, Compact Letter Display (CLD) summaries, and generates boxplots annotated with CLD letters for taxa abundances grouped by a chosen metadata variable.
Usage
ezstat(microbiome_data, metadata, level, selected_metadata)
Arguments
microbiome_data |
Character; path to the microbiome abundance table (CSV, TSV, XLS, or XLSX). |
metadata |
Character; path to the sample metadata file (CSV, TXT, XLS, or XLSX). |
level |
Character; taxonomic rank to aggregate at (e.g. "genus", "g"). |
selected_metadata |
Character; name of the categorical metadata column to group by. |
Details
This function first calls ezclean to produce a cleaned, merged table of sample IDs, metadata, and taxa abundances at the requested taxonomic level. It then:
Runs Kruskal_Wallis tests on each taxon and writes results with FDR_correction.
Performs Dunns pairwise post_hoc tests (BH_adjusted) for taxa with KW p less than or equal to 0.05.
Computes CLD letters for significantly different groups and writes a summary Excel.
Generates high-resolution (900 dpi) boxplots annotated with CLD letters.
Value
Invisibly returns the data.frame
of cleaned sample_taxa abundances used for all analyses.
Examples
## Not run:
mb <- system.file("extdata", "microbiome.csv", package = "mbX")
md <- system.file("extdata", "metadata.csv", package = "mbX")
if (nzchar(mb) && nzchar(md)) {
ezstat(mb, md, "genus", "Group")
}
## End(Not run)