subset_dist: Subset Distance Matrix
In jfq3/QsRutils: R Functions Useful for Community Ecology
Description
Usage
Arguments
Details
Value
References
Description
Subsets a distance matrix.
Usage
1
subset_dist(physeq, d.matrix)
Arguments
physeq
An experiment level phyloseq object.
d.matrix
A distance matrix.
Details
Some distance matrices take a long time to calculate for large data sets. This is especially true of unifrac and generalized unifrac distances calculated by GUniFracs. If distances are first calculated from data in a large experiment level phyloseq object and then it is desired to perform PERMANOVA (with adonis) on a subset of that object, this function provides a means of sub-setting the distance matrix so that it does not have to be calculated again for the subset data. The arguments are the distance matrix for the original phyloseq object and the smaller phyloseq object subset from the original.
Value
A distance matrix of smaller dimensions.
References
Chen J, Bittinger K, Charlson ES et al. (2012) Associating microbiome composition with environmental covariates using generalized UniFrac distances. Bioinformatics, 28, 2106-2113.
jfq3/QsRutils documentation built on Jan. 18, 2021, 12:40 a.m.
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Description Usage Arguments Details Value References
Description
Subsets a distance matrix.
Usage
1 | subset_dist(physeq, d.matrix)
|
Arguments
physeq |
An experiment level phyloseq object. |
d.matrix |
A distance matrix. |
Details
Some distance matrices take a long time to calculate for large data sets. This is especially true of unifrac and generalized unifrac distances calculated by GUniFracs. If distances are first calculated from data in a large experiment level phyloseq object and then it is desired to perform PERMANOVA (with adonis) on a subset of that object, this function provides a means of sub-setting the distance matrix so that it does not have to be calculated again for the subset data. The arguments are the distance matrix for the original phyloseq object and the smaller phyloseq object subset from the original.
Value
A distance matrix of smaller dimensions.
References
Chen J, Bittinger K, Charlson ES et al. (2012) Associating microbiome composition with environmental covariates using generalized UniFrac distances. Bioinformatics, 28, 2106-2113.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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