accu_samp_threshold: Compute the number of sequence to obtain a given proportion...

In adrientaudiere/MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Compute the number of sequence to obtain a given proportion of ASV in accumulation curves

Description

Note that as most bioinformatic pipeline discard singleton, accumulation curves from metabarcoding cannot be interpreted in the same way as with conventional biodiversity sampling techniques.

Usage

accu_samp_threshold(res_accuplot, threshold = 0.95)

Arguments

res_accuplot	the result of the function accu_plot()
threshold	the proportion of ASV to obtain in each samples

Value

a value for each sample of the number of sequences needed to obtain threshold proportion of the ASV

Author(s)

Adrien Taudière

See Also

accu_plot()

Examples

data("GlobalPatterns", package = "phyloseq")
GP <- subset_taxa(GlobalPatterns, GlobalPatterns@tax_table[, 1] == "Archaea")
GP <- rarefy_even_depth(subset_samples_pq(GP, sample_sums(GP) > 3000))
p <- accu_plot(GP, "SampleType", add_nb_seq = TRUE, by.fact = TRUE, step = 10)

val_threshold <- accu_samp_threshold(p)

summary(val_threshold)

##'  Plot the number of sequences needed to accumulate 0.95% of ASV in 50%, 75%
##'  and 100% of samples
p + geom_vline(xintercept = quantile(val_threshold, probs = c(0.50, 0.75, 1)))

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