dist_pos_control: Calculate ecological distance among positive controls vs...

In adrientaudiere/MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Calculate ecological distance among positive controls vs distance for all samples

Description

Compute distance among positive controls, i.e. samples which are duplicated to test for variation, for example in (i) a step in the sampling, (ii) a step in the extraction, (iii) a step in the sequencing.

Usage

dist_pos_control(physeq, samples_names, method = "bray")

Arguments

physeq	(required): a phyloseq-class object obtained using the phyloseq package.
samples_names	(required) a vector of names for samples with positives controls of the same samples having the same name
method	(default: "bray") a method to calculate the distance, parsed to vegan::vegdist(). See ?vegdist for a list of possible values.

Value

A list of two data-frames with (i) the distance among positive controls and (ii) the distance among all samples

Author(s)

Adrien Taudière

Examples

data("enterotype")
sam_name_factice <- gsub("TS1_V2", "TS10_V2", sample_names(enterotype))
res_dist_cont <- dist_pos_control(enterotype, sam_name_factice)
hist(unlist(res_dist_cont$distAllSamples))
abline(
  v = mean(unlist(res_dist_cont$dist_controlontrolSamples), na.rm = TRUE),
  col = "red", lwd = 3
)

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