are_modality_even_depth: Test if the mean number of sequences by samples is link to...

In adrientaudiere/MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Test if the mean number of sequences by samples is link to the modality of a factor

Description

The aim of this function is to provide a warnings if samples depth significantly vary among the modalities of a factor present in the sam_data slot.

This function apply a Kruskal-Wallis rank sum test to the number of sequences per samples in function of the factor fact.

Usage

are_modality_even_depth(physeq, fact, boxplot = FALSE)

Arguments

physeq	(required): a phyloseq-class object obtained using the phyloseq package.
fact	(required): Name of the factor to cluster samples by modalities. Need to be in physeq@sam_data.
boxplot	(logical) Do you want to plot boxplot?

Value

The result of a Kruskal-Wallis rank sum test

Author(s)

Adrien Taudière

Examples

are_modality_even_depth(data_fungi_mini, "Time")$p.value
are_modality_even_depth(rarefy_even_depth(data_fungi_mini), "Time")$p.value
are_modality_even_depth(data_fungi_mini, "Height", boxplot = TRUE)

adrientaudiere/MiscMetabar documentation built on Oct. 13, 2024, 9:42 p.m.