GUniFrac (version 1.2)

Rarefy: Rarefy the OTU table to an equal sequencing depth

Description

GUniFrac is also sensitive to different sequencing depth. To compare microbiomes on an equal basis, rarefaction might be used.

Usage

Rarefy(otu.tab, depth = min(rowSums(otu.tab)))

Arguments

otu.tab

OTU count table, row - n sample, column - q OTU

depth

Required sequencing depth; If not specified, the lowest sequencing depth is used.

Value

Return a LIST containing:

otu.tab.rff

Rarefied OTU table

discard

IDs of samples that does not reach the specified sequencing depth

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References

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

See Also

GUniFrac, PermanovaG

Examples

# NOT RUN {
data(throat.otu.tab)
# Rarefaction
otu.tab.rff <- Rarefy(throat.otu.tab, 1024)$otu.tab.rff
# }