ivar2index

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

counts

A numeric scalar. Specifies reference feature(s)
for additive log-ratio transformation. The argument will also
accept feature name(s) instead of the index position(s).
Set to "iqlr" to use inter-quartile log-ratio transformation.
Ignore to use centered log-ratio transformation.

ivar

This function builds an index from the <code>ivar</code> argument. Used by
 the <code>propr</code> initialize method and <code>updateF</code>.

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.

ivar2index: Build Index from ivar Argument

Description

Usage

Arguments