The bioinformatic evaluation of gene co-expression often begins with correlation-based analyses. However, this approach lacks statistical validity 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>] and rho [Erb and Notredame (2016) <doi:10.1007/s12064-015-0220-8>], to provide 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.
| Version: | 3.0.4 |
| Depends: | methods, R (≥ 3.2.2) |
| Imports: | fastcluster, ggplot2, grDevices, igraph, Rcpp, stats, utils |
| LinkingTo: | Rcpp |
| Suggests: | ALDEx2, cccrm, compositions, data.table, datasets, directlabels, grid, ggdendro, knitr, limma, plotly, reshape2, rgl, rmarkdown, SDMTools, testthat |
| Published: | 2017-06-02 |
| Author: | Thomas Quinn [aut, cre], David Lovell [aut], Ionas Erb [aut], Anders Bilgrau [ctb], Greg Gloor [ctb] |
| Maintainer: | Thomas Quinn <contacttomquinn at gmail.com> |
| BugReports: | http://github.com/tpq/propr/issues |
| License: | GPL-2 |
| URL: | http://github.com/tpq/propr |
| NeedsCompilation: | yes |
| Citation: | propr citation info |
| Materials: | README NEWS |
| CRAN checks: | propr results |
| Reference manual: | propr.pdf |
| Vignettes: |
1. Calculating the Proportionality Coefficients of Compositional Data 2. Understanding RNA-seq Data through Proportionality Analysis 3. How Proportional Is Proportional Enough? 4. Calculating Differential Proportionality Frequently Asked Questions |
| Package source: | propr_3.0.4.tar.gz |
| Windows binaries: | r-devel: propr_3.0.4.zip, r-release: propr_3.0.4.zip, r-oldrel: propr_3.0.4.zip |
| OS X El Capitan binaries: | r-release: propr_3.0.4.tgz |
| OS X Mavericks binaries: | r-oldrel: propr_2.1.8.tgz |
| Old sources: | propr archive |
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