physeq_list_betaDiv: calculating beta diversity for a list of phyloseq objects

Description Usage Arguments Details Value Examples

View source: R/BD_ordinations.R

Description

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

Usage

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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

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

## End(Not run)

HTSSIP documentation built on May 15, 2018, 9:03 a.m.