getGroupsFromDesign

This function splits the input matrix(es) based on a design matrix, into a named list of subsetted matrices. If the design matrix has no names, this function will create names for the resulting list of matrices.

Performs differential correlation analysis on input
matrices, with multiple conditions specified by a design matrix. Contains
functions to filter, process, save, visualize, and interpret differential
correlations of identifier-pairs across the entire identifier space, or with
respect to a particular set of identifiers (e.g., one). Also contains several
functions to perform differential correlation analysis on clusters (i.e., modules)
or genes. Finally, it contains functions to generate empirical p-values for the
hypothesis tests and adjust them for multiple comparisons. Although the package
was built with gene expression data in mind, it is applicable to other types of
genomics data as well, in addition to being potentially applicable to data from
other fields entirely. It is described more fully in the manuscript
introducing it, freely available at <doi:10.1186/s12918-016-0349-1>.

Andrew McKenzie

DGCA

Differential Gene Correlation Analysis

getGroupsFromDesign function

<dl><dt>inputMat</dt>
<dd>Input (e.g., expression) matrix which will be subsetted.</dd>
<dt>design</dt>
<dd>Standard design matrix, must specify at least two conditions. For more info, see ?model.matrix</dd>
<dt>inputMatB</dt>
<dd>Optional input (e.g., expression) matrix which will be subsetted in the same way.</dd>
<dt>secondMat</dt>
<dd>Logical value indicating whether there is a second input matrix to be subsetted.</dd></dl>

Arguments

Split input matrix(es) based on the design matrix. — getGroupsFromDesign

<dl>

<dt>inputMat</dt>
<dd>Input (e.g., expression) matrix which will be subsetted.</dd>


<dt>design</dt>
<dd>Standard design matrix, must specify at least two conditions. For more info, see ?model.matrix</dd>


<dt>inputMatB</dt>
<dd>Optional input (e.g., expression) matrix which will be subsetted in the same way.</dd>


<dt>secondMat</dt>
<dd>Logical value indicating whether there is a second input matrix to be subsetted.</dd>

</dl>

getGroupsFromDesign: Split input matrix(es) based on the design matrix.

Description

Usage

Value

Arguments

Examples