custom_rarefaction: Rarefy a phyloseq object to a custom sample depth and with...

In gauravsk/ranacapa: Utility Functions and 'shiny' App for Simple Environmental DNA Visualizations and Analyses

Description

Rarefy a phyloseq object to a custom sample depth and with given number of repliactes

Usage

custom_rarefaction(physeq_object, sample_size = 10000, replicates = 10,
  ...)

Arguments

physeq_object	A phyloseq class object to be rarefied
sample_size	Desired depth of rarefaction
replicates	Desired number of times to resample from community
...	Other options for phyloseq function rarefy_even_depth

Value

phyloseq class object

Examples

good_taxon_table <- data.frame(sum.taxonomy = c("a;b;c;d;f;u", "p;q;r;s;t;u"),
 site_1 = c(0,1), site_2 = c(10, 20))
good_maps <- data.frame(site = c("site_1", "site_2"),
 season = c("wet", "dry"), host = c("oak", "sage"))
physeq_object <- convert_anacapa_to_phyloseq(good_taxon_table, good_maps)
custom_rarefaction(physeq_object, sample_size = 10, replicates = 1)

gauravsk/ranacapa documentation built on June 7, 2019, 4:03 a.m.