Rarefy {GUniFrac} | R Documentation |
GUniFrac is also sensitive to different sequencing depth. To compare microbiomes on an equal basis, rarefaction might be used.
Rarefy(otu.tab, depth = min(rowSums(otu.tab)))
otu.tab |
OTU count table, row - n sample, column - q OTU |
depth |
Required sequencing depth; If not specified, the lowest sequencing depth is used. |
Return a LIST containing:
otu.tab.rff |
Rarefied OTU table |
discard |
IDs of samples that does not reach the specified sequencing depth |
Jun Chen <chen.jun2@mayo.edu>
Jun Chen et al. (2012). Associating microbiome composition with environmental covariates using generalized UniFrac distances. 28(16): 2106–2113.
data(throat.otu.tab) # Rarefaction otu.tab.rff <- Rarefy(throat.otu.tab, 1024)$otu.tab.rff