propr

Calculating Proportionality Between Vectors of Compositional Data

The bioinformatic evaluation of gene co-expression often begins with correlation-based analyses. However, correlation lacks validity when applied to relative data, including count data generated by next-generation sequencing. 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.

Total

16,876

Last month

541

Last week

119

Average per day

18

Daily downloads

Total downloads

Description file content

Package
propr
Title
Calculating Proportionality Between Vectors of Compositional Data
Version
4.1.6
URL
BugReports
http://github.com/tpq/propr/issues
Description
The bioinformatic evaluation of gene co-expression often begins with correlation-based analyses. However, correlation lacks validity when applied to relative data, including count data generated by next-generation sequencing. This package implements several metrics for proportionality, including phi [Lovell et al (2015) ] and rho [Erb and Notredame (2016) ]. This package also implements several metrics for differential proportionality. Unlike correlation, these measures give the same result for both relative and absolute data.
License
GPL-2
LazyData
true
VignetteBuilder
knitr
RoxygenNote
6.1.0
Encoding
UTF-8
Depends
methods, R (>= 3.2.2)
Imports
fastcluster, ggplot2, grDevices, igraph, Rcpp, stats, utils
Suggests
ALDEx2, Biobase, cccrm, compositions, data.table, datasets, grid, ggdendro, knitr, limma, plotly, reshape2, rgl, rmarkdown, SDMTools, testthat, vegan
LinkingTo
Rcpp
NeedsCompilation
yes
Packaged
2019-07-10 04:34:32 UTC; thom
Author
Thomas Quinn [aut, cre], David Lovell [aut], Ionas Erb [aut], Anders Bilgrau [ctb], Greg Gloor [ctb]
Maintainer
Thomas Quinn
Repository
CRAN
Date/Publication
2019-07-10 05:00:03 UTC

install.packages('propr')

4.1.6

8 days ago

http://github.com/tpq/propr

Thomas Quinn

GPL-2

Depends on

methods, R (>= 3.2.2)

Imports

fastcluster, ggplot2, grDevices, igraph, Rcpp, stats, utils

Suggests

ALDEx2, Biobase, cccrm, compositions, data.table, datasets, grid, ggdendro, knitr, limma, plotly, reshape2, rgl, rmarkdown, SDMTools, testthat, vegan

Discussions