Rarefy {GUniFrac}

Rarefy a Count Table to 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

Author(s)

Jun Chen <[e-mail]>

References

Chen, J., Bittinger, K., Charlson, E.S., Hoffmann, C., Lewis, J., Wu, G.D., Collman, R.G., Bushman, F.D. and Li, H. (2012). Associating microbiome composition with environmental covariates using generalized UniFrac distances. 28(16): 2106–2113.

Examples

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