Hi, I am a little bit confused about the Jaccard distance matrix in phyloseq R package.
distance(esophagus, "jaccard", binary = TRUE) # vegdist jaccard
What is the meaning of binary = TRUE here?
It is not clear to me from the phyloseq package details.
Also, can we write: distance(esophagus, "bray", binary = TRUE)
Thank you for your assistance.
1 answer
Hi,
If you specify jaccard as method, phyloseq will use the vegdist() function from the vegan R package (see source code line 237).
The argument binary = TRUE is an extra parameter, which in the function distance() from phyloseq appears represented by the three dots, i.e., .... These extra arguments will be passed to the function vegdist() (see source code line 138).
Therefore, the argument binary = TRUE according to the ?vegan::vegdist() means the following (see the link):
Perform presence/absence standardization before analysis using decostand.
I hope this answers your question.
António
Log in to answer this question.
-
diff_robust is TRUE but passed_ss is FALSE?
written by sumin •
-
Annotating Illumna epic probes
written by ramiro.barrantes •
-
How to cluster microbial samples after principal coordinate analysis based on beta-diversity
written by Bertalan_Takacs •
-
EdgeR cannot be updated
written by thomas.heigl •
-
Genetic matrix to STRUCTURE file
written by akoontz11 •
-
How to add customized distance to ComplexHeatmap
written by huynguyen96.dnu •
-
Please help to address the BiocCheck NOTEs
written by Pijush Das •
-
Explanation of the markov chain in the given plot.
written by kirannbishwa01
-
Why are gene expression phylogenies and the structure of hierarchical clustering so different?
written by haoyan14ioz •
-
error installing cummerbund in R studio
written by sangita_b
