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

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

Adrien Taudière

Examples


are_modality_even_depth(data_fungi_mini, "Time")$p.value
#> [1] 0.0006936505
are_modality_even_depth(rarefy_even_depth(data_fungi_mini), "Time")$p.value
#> You set `rngseed` to FALSE. Make sure you've set & recorded
#>  the random seed of your session for reproducibility.
#> See `?set.seed`
#> ...
#> 7OTUs were removed because they are no longer 
#> present in any sample after random subsampling
#> ...
#> All modality were undoubtedly rarefy in the physeq object.
#> [1] 1
are_modality_even_depth(data_fungi_mini, "Height", boxplot = TRUE)

#> 
#> 	Kruskal-Wallis rank sum test
#> 
#> data:  nb_seq by fact
#> Kruskal-Wallis chi-squared = 1.1143, df = 2, p-value = 0.5728
#>