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.
|Author||Thomas Quinn [aut, cre], David Lovell [aut], Anders Bilgrau [ctb], Ionas Erb [ctb]|
|Date of publication||2016-12-22 00:50:40|
|Maintainer||Thomas Quinn <firstname.lastname@example.org>|
abstract: Abstract Two propr Objects
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
lrmodel-class: An S4 class to hold results from proportionality analysis.
mail: Mock Mail Count Data
modelCLR: Encapsulate a clr-Transformation
multiplot: Plot Multiple Graphs
packageCheck: Package Check
plotCheck: Plot Check
promptCheck: Feature Check
prop2prob: Calculate Probability from 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