getEnrichmentInter: Create interactive table of gene set enrichment results from...

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

Create interactive table of gene set enrichment results from 'K2' object

Description

Create table gene set enrichment results from 'K2' object.

Usage

getEnrichmentInter(
  K2res,
  maxFDR_score = 0.01,
  minDiff_score = NULL,
  maxPval_score = NULL,
  maxFDR_fisher = NULL,
  maxPval_fisher = NULL,
  gsNames = NULL,
  nodes = NULL,
  pagelength = 50
)

Arguments

K2res	A K2 class object.
maxFDR_score	Numeric. A value between 0 and 1 indicating the FDR cutoff for differential analysis of enrichment scores.
minDiff_score	Numeric. A value between 0 and 1 indicating the mean difference cutoff for differential analysis of enrichment scores.
maxPval_score	Numeric. A value between 0 and 1 indicating the p-value cutoff for differential analysis of enrichment scores.
maxFDR_fisher	Numeric. A value between 0 and 1 indicating the FDR cutoff for Fisher-based overrepresentation analysis.
maxPval_fisher	Numeric. A value between 0 and 1 indicating the p-value cutoff for Fisher-based overrepresentation analysis.
gsNames	Character. A vector of gene sets identifiers to display.
nodes	Character. A vector of node identifiers to display.
pagelength	Numeric. Number of rows to display in each page of output.

Value

An interactive data frame with the following columns:

• Gene Set: The identifier of the gene set.

• Node: The identifier of the partition

• Edge: The identifier of partition subgroup

• Direction: The direction of coefficient for the assigned gene sets

• P Value Fisher: The p-value estimated by Fisher-based overrepresentation analysis

• FDR Fisher: The multiple hypothesis corrected FDR Fisher p-value, adjusted across all partitions

• N Overlap: The intersection of differentially expressed genes and gene set

• N Sig. Genes: The number differentially expressed genes

• N Gene Set: The number genes comprising the gene set

• P Value Score: The p-value estimated by differential analysis of enrichment scores

• FDR Score: The multiple hypothesis corrected FDR p-value estimated by differential analysis of enrichment scores, adjusted across all partitions

• Diff Score: The difference between the mean enrichment score of each subgroup at a given partition

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