alphaTheta

A data.frame or matrix. A "count matrix" with
subjects as rows and features as columns.

counts

A character vector. Group or sub-group memberships,
ordered according to the row names in <code>counts</code>.

group

A double. See vignette for details. Leave missing
to skip Box-Cox transformation.

alpha

Calculate differential proportionality measure, theta,
 using the Box-Cox transformation method.

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 several metrics for proportionality, including
phi [Lovell et al (2015) <DOI:10.1371/journal.pcbi.1004075>] and
rho [Erb and Notredame (2016) <DOI:10.1007/s12064-015-0220-8>]. This package also
implements several metrics for differential proportionality. Unlike correlation,
these measures give the same result for both relative and absolute data.

alphaTheta: Calculate alpha Theta

Description

Usage

Arguments