alphaThetaW_old

A data.frame or matrix. A "count matrix" with
subjects as rows and features as columns. Note that this matrix
does not necessarily have to contain counts.

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

A matrix. Pre-computed <code>limma</code>-based
weights. Optional parameter.

weights

Do not use this function. For testing purposes only.

The bioinformatic evaluation of gene co-expression often begins with
correlation-based analyses. However, correlation lacks validity when
applied to relative data, including count data generated by next-generation
sequencing. 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.

alphaThetaW_old: Calculate Weighted Theta

Description

Usage

Arguments