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], Ionas Erb [ctb], Anders Bilgrau [ctb], Greg Gloor [ctb]
Date of publication2017-03-09 08:18:37
MaintainerThomas Quinn <contacttomquinn@gmail.com>
LicenseGPL-2
Version2.1.8
http://github.com/tpq/propr

View on CRAN

Functions

abstract Man page
adjacent Man page
aldex2propr Man page
aldex.cor Man page
bokeh Man page
bucket Man page
caneToad.counts Man page
caneToad.groups Man page
cytescape Man page
dendroCheck Man page
dendrogram Man page
differentialCheck Man page
ggdend Man page
lr2cor Man page
mail Man page
migraph Man page
migraph.add Man page
migraph.clean Man page
migraph.color Man page
multiplot Man page
packageCheck Man page
pca Man page
perb Man page
phis Man page
phit Man page
plotCheck Man page
plot,propr,missing-method Man page
prism Man page
progress Man page
promptCheck Man page
prop2prob Man page
proportionality Man page
propr Man page
proprALR Man page
[,propr,ANY,ANY-method Man page
propr-class Man page
proprCLR Man page
[,propr-method Man page
proprPairs Man page
proprPerb Man page
proprPhit Man page
proprSym Man page
proprTri Man page
proprVLR Man page
show,propr-method Man page
simplify Man page
slate Man page
smear Man page
snapshot Man page
subset,propr-method Man page
top Man page
visualize Man page

Files

propr
propr/inst
propr/inst/CITATION
propr/inst/doc
propr/inst/doc/questions.html
propr/inst/doc/introduction.R
propr/inst/doc/introduction.html
propr/inst/doc/visualize.html
propr/inst/doc/visualize.Rmd
propr/inst/doc/questions.Rmd
propr/inst/doc/visualize.R
propr/inst/doc/introduction.Rmd
propr/inst/doc/questions.R
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-lr2propr.R
propr/tests/testthat/test-vlr.R
propr/tests/testthat/test-simplify.R
propr/tests/testthat/test-logratio.R
propr/tests/testthat/test-prop2prob.R
propr/tests/testthat/test-phit.R
propr/tests/testthat/test-aldex2propr.R
propr/src
propr/src/backend.cpp
propr/src/init.c
propr/src/RcppExports.cpp
propr/src/lr2propr.cpp
propr/src/backend.h
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/aldex2propr.R propr/R/aldex.cor.R propr/R/methods.R propr/R/RcppExports.R propr/R/deprecated.R propr/R/propr.R propr/R/proprViz.R propr/R/global.R
propr/vignettes
propr/vignettes/visualize.Rmd
propr/vignettes/questions.Rmd
propr/vignettes/introduction.Rmd
propr/README.md
propr/MD5
propr/build
propr/build/vignette.rds
propr/DESCRIPTION
propr/man
propr/man/aldex.cor.Rd propr/man/packageCheck.Rd propr/man/progress.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/migraph.Rd propr/man/proprSym.Rd propr/man/lr2cor.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/plotCheck.Rd propr/man/aldex2propr.Rd propr/man/proprVLR.Rd propr/man/proprPairs.Rd propr/man/proprPerb.Rd

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