Import Unifrac distance matrix to R

[sdpapet]

Hello, has anyone tried to import unifrac distance to R to do some analysis. I use R vegan package a lot, but the command "vegdist" in vegan package doesn't support to build a unifrac distance. I was wondering if it is possible to use R to analyze the unifrac matrix.

~Ben

[Flo]

Hi ben,

The "vegdist" function from the vegan package is usefull in order to calculate pairwise community distance between samples (e.g., euclidean, sorensen, bray-curtis...). You can use the OTU table to compute that kind of distance using "vegdist" function.
The Unifrac matrix is by itself a distance matrix, like a bray-curtis matrix, so I don't clearly understand why you are trying to use the vegdist function on the unifrac matrix!
You can use metaMDS function as an ordinattion method to depict community variations across samples...or capscale function to understand community variations as a function of environnmental variables.

Hope this help!

Flo

[Flo]

http://cran.r-project.org/web/packages/vegan/vignettes/intro-vegan.pdf

[Pet Chiang]

Hi Flo,

Thanks. Yes, I know I can use use vegdist to create different distance matrices (e.g., bray-curtis) and then do ordination analysis. The reason that I want to import unifrac distance to R is I want to use other downstream R workflows and packages. For example, I want to build a cluster based on unfriac (I know Qiime can do this), but R "cluster" package is more powerful.

~Ben

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