propr: Calculating Proportionality Between Vectors of Compositional Data
Version 2.2.0

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) ] and rho [Erb and Notredame (2016) ], 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.

AuthorThomas Quinn [aut, cre], David Lovell [aut], Ionas Erb [ctb], Anders Bilgrau [ctb], Greg Gloor [ctb]
Date of publication2017-04-19 03:58:50 UTC
MaintainerThomas Quinn <contacttomquinn@gmail.com>
LicenseGPL-2
Version2.2.0
URL http://github.com/tpq/propr
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("propr")

Getting started

README.md
Calculating the Proportionality Coefficients of Compositional Data
Frequently Asked Questions
Understanding RNA-seq Data through Proportionality Analysis

Popular man pages

dendroCheck: Dendrogram Plot Check
mail: Mock Mail Count Data
propd: Calculate Differential Proportionality
proportionality: Calculate Proportionality
propr: The propr Package
proprSym: Symmetrizes a proportionality matrix.
visualize: Visualize Proportionality
See all...

All man pages Function index File listing

Man pages

abstract: Abstract Two propr Objects
aldex2propr: Import 'ALDEx2' Object
aldex.cor: Correlate CLR with a Continuous Measurement
caneToad.counts: Example Cane Toad Count Data
caneToad.groups: Example Cane Toad Group Data
dendroCheck: Dendrogram Plot Check
differentialCheck: Differential Proportionality Check
ggdend: Dendrogram Plot Wrapper
lr2cor: Correlate CLR with a Continuous Measurement
mail: Mock Mail Count Data
marg.abs: Example Absolute mRNA
migraph: 'igraph' Helper Functions
multiplot: Plot Multiple Graphs
packageCheck: Package Check
plotCheck: Plot Check
progress: Make Progress Bar
promptCheck: Feature Check
prop2prob: Calculate Probability from Proportionality
propd: Calculate Differential Proportionality
proportionality: Calculate Proportionality
propr: The propr Package
proprALR: Calculates the additive log-ratio transformation.
proprCLR: Calculates the centered log-ratio transformation.
proprPairs: Recasts proportionality matrix as a table of feature pairs.
proprPerb: Calculate proportionality metric rho (Erb 2016).
proprPhit: Calculate proportionality metric phi (Lovell 2015).
proprSym: Symmetrizes a proportionality matrix.
proprTri: Retrieve the lower left triangle of a proportionality matrix.
proprVLR: Calculates the variance of the log of the ratios.
top: Example propr Object
visualize: Visualize Proportionality

Functions

[,propr,ANY,ANY-method Man page
[,propr-method Man page
abstract Man page Source code
adjacent Man page Source code
aldex.cor Man page Source code
aldex2propr Man page Source code
alrRcpp Source code
bokeh Man page Source code
bucket Man page Source code
caneToad.counts Man page
caneToad.groups Man page
clrRcpp Source code
coordToIndex Source code
corRcpp Source code
covRcpp Source code
cytescape Man page Source code
dendroCheck Man page Source code
dendrogram Man page Source code
differentialCheck Man page Source code
ggdend Man page Source code
indexPairs Source code
indexToCoord Source code
initialize,propr-method Man page
labRcpp Source code
linRcpp Source code
lltRcpp Source code
lr2cor Man page Source code
lr2phi Source code
lr2phs Source code
lr2rho Source code
lr2vlr Source code
mail Man page
marg.abs Man page
mds Source code
migraph Man page
migraph.add Man page Source code
migraph.clean Man page Source code
migraph.color Man page Source code
multiplot Man page Source code
packageCheck Man page Source code
pca Man page Source code
perb Man page Source code
phiRcpp Source code
phis Man page Source code
phit Man page Source code
plot,propr,missing-method Man page
plotCheck Man page Source code
prism Man page Source code
progress Man page Source code
promptCheck Man page Source code
prop2prob Man page Source code
propd Man page
proportionality Man page
propr Man page
propr-class Man page
proprALR Man page Source code
proprCLR Man page Source code
proprPairs Man page Source code
proprPerb Man page Source code
proprPhit Man page Source code
proprSym Man page Source code
proprTri Man page Source code
proprVLR Man page Source code
rhoRcpp Source code
show,propr-method Man page
simplify Man page Source code
slate Man page Source code
smear Man page Source code
snapshot Man page Source code
subset,propr-method Man page
symRcpp Source code
top Man page
urtRcpp Source code
visualize Man page
vlrRcpp Source code

Files

inst
inst/CITATION
inst/doc
inst/doc/questions.html
inst/doc/introduction.R
inst/doc/introduction.html
inst/doc/visualize.html
inst/doc/visualize.Rmd
inst/doc/questions.Rmd
inst/doc/visualize.R
inst/doc/introduction.Rmd
inst/doc/questions.R
tests
tests/testthat.R
tests/testthat
tests/testthat/test-linRcpp.R
tests/testthat/test-perb.R
tests/testthat/test-Rcpp.R
tests/testthat/test-phis.R
tests/testthat/test-lr2propr.R
tests/testthat/test-vlr.R
tests/testthat/test-simplify.R
tests/testthat/test-logratio.R
tests/testthat/test-prop2prob.R
tests/testthat/test-phit.R
tests/testthat/test-aldex2propr.R
src
src/backend.cpp
src/init.c
src/RcppExports.cpp
src/lr2propr.cpp
src/backend.h
NAMESPACE
NEWS.md
data
data/mail.rda
data/caneToad.counts.rda
data/caneToad.groups.rda
data/datalist
data/marg.abs.rda
data/top.rda
R
R/propd.R
R/prop2prob.R
R/aldex2propr.R
R/aldex.cor.R
R/methods.R
R/RcppExports.R
R/deprecated.R
R/propr.R
R/proprViz.R
R/global.R
vignettes
vignettes/visualize.Rmd
vignettes/questions.Rmd
vignettes/introduction.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/aldex.cor.Rd
man/packageCheck.Rd
man/marg.abs.Rd
man/progress.Rd
man/differentialCheck.Rd
man/ggdend.Rd
man/proportionality.Rd
man/prop2prob.Rd
man/dendroCheck.Rd
man/proprCLR.Rd
man/migraph.Rd
man/proprSym.Rd
man/lr2cor.Rd
man/top.Rd
man/proprPhit.Rd
man/proprALR.Rd
man/caneToad.counts.Rd
man/abstract.Rd
man/caneToad.groups.Rd
man/proprTri.Rd
man/propr.Rd
man/promptCheck.Rd
man/multiplot.Rd
man/mail.Rd
man/visualize.Rd
man/plotCheck.Rd
man/aldex2propr.Rd
man/propd.Rd
man/proprVLR.Rd
man/proprPairs.Rd
man/proprPerb.Rd
propr documentation built on May 19, 2017, 7:01 a.m.

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