propr: Calculating Proportionality Between Vectors of Compositional Data

Share:

The bioinformatic evaluation of gene co-expression often begins with correlation-based analyses. However, this approach lacks statistical validity when applied to relative data, including those biological count data produced by microarray assays or high-throughput RNA-sequencing. 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 the calculation of feature dependence through proportionality, as discussed in the cited publications.

Author
Thomas Quinn [aut, cre], David Lovell [aut]
Date of publication
2016-10-31 07:57:10
Maintainer
Thomas Quinn <contacttomquinn@gmail.com>
License
GPL-2
Version
2.0.4
URLs

View on CRAN

Man pages

bokeh
Make Bokeh Plot
bucket
Make Bucket Plot
caneToad.counts
Example Cane Toad Count Data
caneToad.groups
Example Cane Toad Group Data
mds
Make MDS Plot
perb
Calculate proportionality metric rho.
phit
Calculate proportionality metric phi.
plotCheck
Plot Check
prism
Make Prism Plot
propr
The propr Package
proprALR
Calculates the additive log-ratio transformation.
propr-class
An S4 class to hold results from proportionality analysis.
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.
simplify
Simplify Indexed Matrix
slate
Build 'propr' Table
snapshot
Make Snapshot Plot
top
Example propr Object

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-perb.R
propr/tests/testthat/test-Rcpp.R
propr/tests/testthat/test-vlr.R
propr/tests/testthat/test-simplify.R
propr/tests/testthat/test-logratio.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/caneToad.counts.rda
propr/data/caneToad.groups.rda
propr/data/datalist
propr/data/top.rda
propr/R
propr/R/classes.R
propr/R/plot.R
propr/R/methods.R
propr/R/simplify.R
propr/R/perb.R
propr/R/RcppExports.R
propr/R/deprecated.R
propr/R/phit.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/bokeh.Rd
propr/man/propr-class.Rd
propr/man/perb.Rd
propr/man/prism.Rd
propr/man/proprCLR.Rd
propr/man/proprSym.Rd
propr/man/top.Rd
propr/man/snapshot.Rd
propr/man/proprPhit.Rd
propr/man/proprALR.Rd
propr/man/caneToad.counts.Rd
propr/man/caneToad.groups.Rd
propr/man/proprTri.Rd
propr/man/propr.Rd
propr/man/mds.Rd
propr/man/phit.Rd
propr/man/slate.Rd
propr/man/plotCheck.Rd
propr/man/simplify.Rd
propr/man/proprVLR.Rd
propr/man/proprPairs.Rd
propr/man/proprPerb.Rd
propr/man/bucket.Rd