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

Value

Return a LIST containing:

Author(s)

Jun Chen <chenjun@mail.med.upenn.edu>

References

Jun Chen and Hongzhe Li(2012). Associating microbiome composition with environmental covariates using generalized UniFrac distances. (Submitted)

See Also

GUniFrac, PermanovaG

Examples

data(throat.otu.tab)
# Rarefaction
otu.tab.rff <- Rarefy(throat.otu.tab, 1024)$otu.tab.rff

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(GUniFrac)
Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-0
Loading required package: ape
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/GUniFrac/Rarefy.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Rarefy
> ### Title: Rarefy the OTU table to an equal sequencing depth
> ### Aliases: Rarefy
> ### Keywords: Rarefaction Ecology
> 
> ### ** Examples
> 
> data(throat.otu.tab)
> # Rarefaction
> otu.tab.rff <- Rarefy(throat.otu.tab, 1024)$otu.tab.rff
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>