adjustPVals

Wraps around the R base implementation of p.adjust, as well as the methods used in the fdr tool package.

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

adjustPVals function

<dl><dt>pVals</dt>
<dd>Numeric vector of p-values to adjust.</dd>
<dt>adjust</dt>
<dd>Allows for resulting p-values to be corrected for multiple hypothesis tests. Optional and some non-default choices require the "fdrtool" package. Default = "none", which means that no p-value adjustment is performed. Other options include methods in ?p.adjust (i.e., "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr"), and methods in ?fdrtool (i.e., "fndr", "pct0", "locfdr").</dd>
<dt>plotFdr</dt>
<dd>Allows for plotting of fdrtool p-value adjustment result, if this is chosen. Requires fdrtool package. Default = FALSE.</dd>
<dt>verbose</dt>
<dd>If TRUE, the function prints out the general method used for multiple correction analysis. Default = FALSE.</dd></dl>

Arguments

Adjusts a numeric vector of p-values. — adjustPVals

<dl>

<dt>pVals</dt>
<dd>Numeric vector of p-values to adjust.</dd>


<dt>adjust</dt>
<dd>Allows for resulting p-values to be corrected for multiple hypothesis tests. Optional and some non-default choices require the "fdrtool" package. Default = "none", which means that no p-value adjustment is performed. Other options include methods in ?p.adjust (i.e., "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr"), and methods in ?fdrtool (i.e., "fndr", "pct0", "locfdr").</dd>


<dt>plotFdr</dt>
<dd>Allows for plotting of fdrtool p-value adjustment result, if this is chosen. Requires fdrtool package. Default = FALSE.</dd>


<dt>verbose</dt>
<dd>If TRUE, the function prints out the general method used for multiple correction analysis. Default = FALSE.</dd>

</dl>

adjustPVals: Adjusts a numeric vector of p-values.

Description

Usage

Value

Arguments

Examples