framework for the calculation of feature dependence through proportionality, as

microarray assays or high-throughput RNA-sequencing. Two metrics of proportionality,
phi [Lovell et al (2015) <DOI:10.1371/journal.pcbi.1004075>] and rho [Erb and
Notredame (2016) <DOI:10.1007/s12064-015-0220-8>], both derived from compositional
data analysis, a branch of math dealing specifically with relative data,
represent novel alternatives to correlation. This package introduces a programmatic

Suggests: compositions, dendextend, fastcluster, ggplot2, ggthemes,

person("David", "Lovell", email = "david.lovell@qut.edu.au", role = "aut"),
person("Anders", "Bilgrau", email = "anders.ellern.bilgrau@gmail.com", role = "ctb"),
person("Ionas", "Erb", email = "ionas.erb@crg.eu", role = "ctb")
when applied to relative count data. This includes, for example, biological data
produced by high-throughput RNA-sequencing, chromatin immunoprecipitation (ChIP),
ChIP-sequencing, Methyl-Capture sequencing, and other techniques. Two metrics of
proportionality, phi [Lovell et al (2015) <DOI:10.1371/journal.pcbi.1004075>]
and rho [Erb and Notredame (2016) <DOI:10.1007/s12064-015-0220-8>], both derived
from compositional data analysis, a branch of math dealing specifically with
relative data, represent novel alternatives to correlation. This package
introduces a programmatic framework for calculating feature dependence through
proportionality, as discussed in the cited publications.
Imports: fastcluster, ggplot2, methods, Rcpp, stats, utils
Suggests: cccrm, compositions, data.table, grid, ggdendro, igraph,
knitr, plotly, reshape2, rmarkdown, testthat

person("Ionas", "Erb", email = "ionas.erb@crg.eu", role = "ctb"),
person("Greg", "Gloor", email = "ggloor@uwo.ca", role = "ctb")
Imports: fastcluster, ggplot2, igraph, methods, Rcpp, stats, utils
Suggests: ALDEx2, cccrm, compositions, data.table, grid, ggdendro,
knitr, plotly, reshape2, rgl, rmarkdown, testthat

when applied to relative data. This includes, for example, biological count data
generated by high-throughput RNA-sequencing, chromatin immunoprecipitation (ChIP),
ChIP-sequencing, Methyl-Capture sequencing, and other techniques. This package
implements two metrics, phi [Lovell et al (2015) <DOI:10.1371/journal.pcbi.1004075>]
a valid alternatives to correlation for relative data. Unlike correlation, these
metrics give the same result for both relative and absolute data. Pairs that are
strongly proportional in relative space are also strongly correlated in absolute
space. Proportionality avoids the pitfall of spurious correlation.
Imports: fastcluster, ggplot2, igraph, Rcpp, stats, utils