physeq_list_betaDiv: calculating beta diversity for a list of phyloseq objects

In nick-youngblut/HTSSIP: High Throughput Sequencing of Stable Isotope Probing Data Analysis

Description

For each phyloseq object in a list, calculates beta-diversity between all samples using the phyloseq::distance function.

Usage

physeq_list_betaDiv(physeq_l, method = "unifrac", weighted = TRUE,
  fast = TRUE, normalized = TRUE, parallel = FALSE)

Arguments

physeq_l	A list of phyloseq objects
method	See phyloseq::distance
weighted	Weighted Unifrac (if calculating Unifrac)
fast	Fast calculation method
normalized	Normalized abundances
parallel	Calculate in parallel

Details

Note: for calculating Unifrac values, phyloseq will select a root at random if the input phylogeny is not rooted.

Value

List of dist objects

Examples

data(physeq_S2D2_l)
## Not run: 
physeq_S2D2_l_d = physeq_list_betaDiv(physeq_S2D2_l)

## End(Not run)

nick-youngblut/HTSSIP documentation built on May 23, 2019, 4:46 p.m.