proportionality: Proportionality Distance

Description Usage Arguments Value References See Also Examples

View source: R/proprotionality.R

Description

proportionality is a wrapper that compute proportionality distance for a clustering result (pca, spca, pls, spls, block.pls, block.spls). and it performs a u-test to compare the median within a cluster to the median of the entire background set.

Usage

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Arguments

X

an object of the class: pca, spca, pls, spls, block.pls or block.spls

Value

Return a list containing the following components:

propr.distance

Square matrix with proportionality distance between pairs of features

propr.distance.w.cluster

distance between pairs with cluster label

pvalue

Wilcoxon U-test p-value comparing the medians within clusters and with the entire background set

References

Lovell, D., Pawlowsky-Glahn, V., Egozcue, J. J., Marguerat, S., Bähler, J. (2015). Proportionality: a valid alternative to correlation for relative data. PLoS Comput. Biol. 11, e1004075. doi: 10.1371/journal.pcbi.1004075

Quinn, T. P., Richardson, M. F., Lovell, D., Crowley, T. M. (2017). propr: an r-package for identifying proportionally abundant features using compositional data analysis. Sci. Rep. 7, 16252. doi: 10.1038/s41598-017-16520-0

See Also

propr

Examples

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demo <- suppressWarnings(get_demo_cluster())

# pca
X <- demo$pca
propr.res <- proportionality(X)
plot(propr.res)

# pls
X <- demo$spls
propr.res <- proportionality(X)
plot(propr.res)

# block.pls
X <- demo$block.spls
propr.res <- proportionality(X)
plot(propr.res)

abodein/timeOmics_BioC documentation built on April 25, 2021, 5:23 p.m.