enrichit_params

Common parameters for enrichit functions

Fast implementations of functional enrichment analysis methods using 'C++' via 'Rcpp'.
Currently provides Over-Representation Analysis (ORA) and Gene Set Enrichment Analysis (GSEA).
The multilevel GSEA algorithm is derived from the 'fgsea' package.
Methods are described in Subramanian et al. (2005) <doi:10.1073/pnas.0506580102> and Korotkevich et al. (2021) <doi:10.1101/060012>.

Guangchuang Yu

enrichit

'C++' Implementations of Functional Enrichment Analysis

enrichit_params function

<dl><dt>geneList</dt>
<dd>A named numeric vector of gene statistics (e.g., log fold change), ranked in descending order.</dd>
<dt>gene_sets</dt>
<dd>A named list of gene sets. Each element is a character vector of genes.</dd>
<dt>nPerm</dt>
<dd>Number of permutations for p-value calculation (default: 1000).</dd>
<dt>exponent</dt>
<dd>Weighting exponent for enrichment score (default: 1.0).</dd>
<dt>minGSSize</dt>
<dd>minimal size of each geneSet for analyzing</dd>
<dt>maxGSSize</dt>
<dd>maximal size of each geneSet for analyzing</dd>
<dt>pvalueCutoff</dt>
<dd>P-value cutoff.</dd>
<dt>pAdjustMethod</dt>
<dd>P-value adjustment method (e.g., "BH").</dd>
<dt>verbose</dt>
<dd>Logical. Print progress messages.</dd>
<dt>gson</dt>
<dd>A GSON object containing gene set information.</dd>
<dt>method</dt>
<dd>Permutation method.</dd>
<dt>adaptive</dt>
<dd>Logical. Use adaptive permutation.</dd>
<dt>minPerm</dt>
<dd>Minimum permutations for adaptive mode.</dd>
<dt>maxPerm</dt>
<dd>Maximum permutations for adaptive mode.</dd>
<dt>pvalThreshold</dt>
<dd>P-value threshold for early stopping.</dd></dl>

Arguments

Common parameters for enrichit functions — enrichit_params

<dl>

<dt>geneList</dt>
<dd>A named numeric vector of gene statistics (e.g., log fold change), ranked in descending order.</dd>


<dt>gene_sets</dt>
<dd>A named list of gene sets. Each element is a character vector of genes.</dd>


<dt>nPerm</dt>
<dd>Number of permutations for p-value calculation (default: 1000).</dd>


<dt>exponent</dt>
<dd>Weighting exponent for enrichment score (default: 1.0).</dd>


<dt>minGSSize</dt>
<dd>minimal size of each geneSet for analyzing</dd>


<dt>maxGSSize</dt>
<dd>maximal size of each geneSet for analyzing</dd>


<dt>pvalueCutoff</dt>
<dd>P-value cutoff.</dd>


<dt>pAdjustMethod</dt>
<dd>P-value adjustment method (e.g., "BH").</dd>


<dt>verbose</dt>
<dd>Logical. Print progress messages.</dd>


<dt>gson</dt>
<dd>A GSON object containing gene set information.</dd>


<dt>method</dt>
<dd>Permutation method.</dd>


<dt>adaptive</dt>
<dd>Logical. Use adaptive permutation.</dd>


<dt>minPerm</dt>
<dd>Minimum permutations for adaptive mode.</dd>


<dt>maxPerm</dt>
<dd>Maximum permutations for adaptive mode.</dd>


<dt>pvalThreshold</dt>
<dd>P-value threshold for early stopping.</dd>

</dl>

enrichit_params: Common parameters for enrichit functions

Description

Arguments