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 several metrics for proportionality, including phi [Lovell et al (2015) <doi:10.1371/journal.pcbi.1004075>] and rho [Erb and Notredame (2016) <doi:10.1007/s12064-015-0220-8>]. This package also implements several metrics for differential proportionality. Unlike correlation, these measures give the same result for both relative and absolute data.
| Version: | 3.1.4 |
| 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: | 2018-01-18 |
| 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. An Introduction to Proportionality 2. Understanding Proportionality through Visualization 3. How Proportional Is Proportional Enough? 4. A Brief Critique of Proportionality 5. An Introduction to Differential Proportionality 6. Moderating Differential Proportionality Frequently Asked Questions |
| Package source: | propr_3.1.4.tar.gz |
| Windows binaries: | r-devel: propr_3.1.4.zip, r-release: propr_3.1.4.zip, r-oldrel: propr_3.1.4.zip |
| OS X El Capitan binaries: | r-release: propr_3.1.4.tgz |
| OS X Mavericks binaries: | r-oldrel: propr_3.1.2.tgz |
| Old sources: | propr archive |
| Reverse suggests: | exprso |
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