getEnrichmentTable: Extract table of enrichment results from 'K2' object

In montilab/K2Taxonomer: Creating annotated submodules of high-throughput data through recursive partitioning

Extract table of enrichment results from 'K2' object

Description

Create table fisher- and gene set scoring enrichment results from 'K2' object.

Usage

getEnrichmentTable(K2res)

Arguments

K2res

A K2 class object.

Value

A data.frame object with the following columns:

• category: The user-specified gene set names

• node: The identifier of the partition

• edge: Indication of which subgroup the gene was assigned at a given partition

• direction: The direction of coefficient for the assigned gene set

• pval_fisher: The p-value of the enrichment test comparing the subgroup-assigned gene set to the user-specified gene set

• fdr_fisher: The multiple hypothesis corrected FDR (Benjamini-Hochberg) p-value of enrichment, adjusted across all partitions

• nhits: The intersection of subgroup-assigned genes and the user-specified gene set

• ndrawn: The number of subgroup-assigned genes

• ncats: The number of genes in the user-specified gene set

• ntot: The background population of possible genes

• pval_limma: The p-value estimated by the 'limma' R package

• fdr_limma: The multiple hypothesis corrected FDR (Benjamini-Hochberg) p-value of differential analysis, adjusted across all partitions

• coef: The difference between the means of each subgroup at a given partition

• mean: The mean across all observations at the given partition

• t: The test statistic estimated by the 'limma' R package

• hits: A comma deliminated string of intersection gene identifers

References

\insertRef

reed_2020K2Taxonomer \insertReflimmaK2Taxonomer \insertRefbhK2Taxonomer \insertRefgsvaK2Taxonomer

montilab/K2Taxonomer documentation built on April 5, 2025, 3:58 a.m.