taxa_only_in_one_level: Show taxa which are present in only one given level of a...

In adrientaudiere/MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Show taxa which are present in only one given level of a modality

Description

Given one modality name in sam_data and one level of the modality, return the taxa strictly specific of this level.

Usage

taxa_only_in_one_level(
  physeq,
  modality,
  level,
  min_nb_seq_taxa = 0,
  min_nb_samples_taxa = 0
)

taxa_only_in_one_level(
  physeq,
  modality,
  level,
  min_nb_seq_taxa = 0,
  min_nb_samples_taxa = 0
)

Arguments

physeq	(required): a phyloseq-class object obtained using the phyloseq package.
modality	(required) The name of a column present in the ⁠@sam_data⁠ slot of the physeq object. Must be a character vector or a factor.
level	(required) The level (must be present in modality) of interest
min_nb_seq_taxa	(default 0 = no filter) The minimum number of sequences per taxa
min_nb_samples_taxa	(default 0 = no filter) The minimum number of samples per taxa

Value

A vector of taxa names

A vector of taxa names

Author(s)

Adrien Taudière

Examples

data_fungi_mini_woNA4height <- subset_samples(
  data_fungi_mini,
  !is.na(data_fungi_mini@sam_data$Height)
)
taxa_only_in_one_level(data_fungi_mini_woNA4height, "Height", "High")
#' # Taxa present only in low height samples
suppressMessages(suppressWarnings(
  taxa_only_in_one_level(data_fungi, "Height", "Low")
))
# Number of taxa present only in sample of time equal to 15
suppressMessages(suppressWarnings(
  length(taxa_only_in_one_level(data_fungi, "Time", "15"))
))
data_fungi_mini_woNA4height <- subset_samples(
  data_fungi_mini,
  !is.na(data_fungi_mini@sam_data$Height)
)
taxa_only_in_one_level(data_fungi_mini_woNA4height, "Height", "High")
#' # Taxa present only in low height samples
suppressMessages(suppressWarnings(
  taxa_only_in_one_level(data_fungi, "Height", "Low")
))
# Number of taxa present only in sample of time equal to 15
suppressMessages(suppressWarnings(
  length(taxa_only_in_one_level(data_fungi, "Time", "15"))
))

adrientaudiere/MiscMetabar documentation built on Dec. 19, 2024, 3:16 a.m.