propr: Calculating Proportionality Between Vectors of Compositional Data

The bioinformatic evaluation of gene co-expression often begins with correlation-based analyses. However, this approach lacks statistical validity 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.

AuthorThomas Quinn [aut, cre], David Lovell [aut], Anders Bilgrau [ctb], Ionas Erb [ctb]
Date of publication2016-12-22 00:50:40
MaintainerThomas Quinn <contacttomquinn@gmail.com>
LicenseGPL-2
Version2.1.1
http://github.com/tpq/propr

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Files in this package

propr
propr/inst
propr/inst/doc
propr/inst/doc/introduction.R
propr/inst/doc/introduction.html
propr/inst/doc/visualize.html
propr/inst/doc/visualize.Rmd
propr/inst/doc/visualize.R
propr/inst/doc/introduction.Rmd
propr/tests
propr/tests/testthat.R
propr/tests/testthat
propr/tests/testthat/test-linRcpp.R
propr/tests/testthat/test-perb.R
propr/tests/testthat/test-Rcpp.R
propr/tests/testthat/test-phis.R
propr/tests/testthat/test-vlr.R
propr/tests/testthat/test-simplify.R
propr/tests/testthat/test-logratio.R
propr/tests/testthat/test-lrmodel.R
propr/tests/testthat/test-prop2prob.R
propr/tests/testthat/test-phit.R
propr/src
propr/src/backend.cpp
propr/src/RcppExports.cpp
propr/NAMESPACE
propr/NEWS.md
propr/data
propr/data/mail.rda
propr/data/caneToad.counts.rda
propr/data/caneToad.groups.rda
propr/data/datalist
propr/data/top.rda
propr/R
propr/R/prop2prob.R propr/R/methods.R propr/R/RcppExports.R propr/R/proportionality.R propr/R/deprecated.R propr/R/lrmodel.R propr/R/visualize.R propr/R/global.R
propr/vignettes
propr/vignettes/visualize.Rmd
propr/vignettes/introduction.Rmd
propr/README.md
propr/MD5
propr/build
propr/build/vignette.rds
propr/DESCRIPTION
propr/man
propr/man/packageCheck.Rd propr/man/differentialCheck.Rd propr/man/ggdend.Rd propr/man/proportionality.Rd propr/man/prop2prob.Rd propr/man/dendroCheck.Rd propr/man/proprCLR.Rd propr/man/proprSym.Rd propr/man/top.Rd propr/man/proprPhit.Rd propr/man/proprALR.Rd propr/man/caneToad.counts.Rd propr/man/abstract.Rd propr/man/caneToad.groups.Rd propr/man/proprTri.Rd propr/man/propr.Rd propr/man/promptCheck.Rd propr/man/multiplot.Rd propr/man/mail.Rd propr/man/visualize.Rd propr/man/lrmodel-class.Rd propr/man/plotCheck.Rd propr/man/modelCLR.Rd propr/man/proprVLR.Rd propr/man/proprPairs.Rd propr/man/proprPerb.Rd

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