GUniFrac (version 1.2)

GUniFrac-package: Generalized UniFrac distance for comparing microbial communities.

Description

A generalized version of the commonly used UniFrac distance. The generalized UniFrac distance contains an extra parameter controlling the weight on abundant lineages so the distance is not dominated by highly abundant lineages. The unweighted and weighted UniFrac, and variance-adjusted weighted UniFrac distances are also implemented. The package also implements a permutation-based multivariate analysis of variance using MULTIPLE distance matrices.

Details

Package:	GUniFrac
Type:	Package
Version:	1.1
Date:	2018-02-14
License:	GPL-3
LazyLoad:	yes

References

Jun Chen et al. (2012). Associating microbiome composition with environmental covariates using generalized UniFrac distances. 28(16): 2106<U+2013>2113.

Examples

# NOT RUN {
data(throat.otu.tab)
data(throat.tree)
data(throat.meta)

groups <- throat.meta$SmokingStatus

# Rarefaction
otu.tab.rff <- Rarefy(throat.otu.tab)$otu.tab.rff

# Calculate the UniFracs
unifracs <- GUniFrac(otu.tab.rff, throat.tree, alpha=c(0, 0.5, 1))$unifracs

dw <- unifracs[, , "d_1"]			# Weighted UniFrac
du <- unifracs[, , "d_UW"]			# Unweighted UniFrac	
dv <- unifracs[, , "d_VAW"]			# Variance adjusted weighted UniFrac
d0 <- unifracs[, , "d_0"]     		# GUniFrac with alpha 0  
d5 <- unifracs[, , "d_0.5"]   		# GUniFrac with alpha 0.5 

# Permanova - Distance based multivariate analysis of variance
adonis(as.dist(d5) ~ groups)

# Combine d(0), d(0.5), d(1) for testing
PermanovaG(unifracs[, , c("d_0", "d_0.5", "d_1")] ~ groups)
# }