Calculate ecological distance among positive controls vs distance for all samples

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

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
)