compare_pairs_pq: Compare samples in pairs using diversity and number of ASV...

In adrientaudiere/MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Compare samples in pairs using diversity and number of ASV including shared ASV.

Description

For the moment refseq slot need to be not Null.

Usage

compare_pairs_pq(
  physeq = NULL,
  bifactor = NULL,
  modality = NULL,
  merge_sample_by = NULL,
  nb_min_seq = 0,
  veg_index = "shannon",
  na_remove = TRUE
)

Arguments

physeq	(required): a phyloseq-class object obtained using the phyloseq package.
bifactor	(required) a factor (present in the sam_data slot of the physeq object) presenting the pair names
modality	the name of the column in the sam_data slot of the physeq object to split samples by pairs
merge_sample_by	a vector to determine which samples to merge using the merge_samples2() function. Need to be in physeq@sam_data
nb_min_seq	minimum number of sequences per sample to count the ASV/OTU
veg_index	(default: "shannon") index for the vegan::diversity function
na_remove	(logical, default TRUE) If set to TRUE, remove samples with NA in the variables set in bifactor, modality and merge_sample_by. NA in variables are well managed even if na_remove = FALSE, so na_remove may be useless.

Value

A tibble with information about the number of shared ASV, shared number of sequences and diversity

Examples

data_fungi_low_high <- subset_samples(data_fungi, Height %in% c("Low", "High"))
compare_pairs_pq(data_fungi_low_high, bifactor = "Height", merge_sample_by = "Height")
compare_pairs_pq(data_fungi_low_high,
  bifactor = "Height",
  merge_sample_by = "Height", modality = "Time"
)

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