sample_data: Sample ontology data

Description Usage Format

Description

Sample data.table containing enrichment results (over-representation, ORA) from different databases, which are:

DO

Disease Ontology

GOBP

Gene Ontology (GO), Biological Process (BP)

GOMF

Gene Ontology (GO), Molecular Function (MF)

GOCC

Gene Ontology (GO), Cellular Component(CC)

KEGG

Kyoto Encyclopedia of Genes and Genomes

MKEGG

KEGG Modules

REACTOME

Reactome

Usage

1

Format

data.table columns for each item in the list contain:

Condition

Comparison made by differential expression analysis (e.g. AvsB: Group A vs. Group B)

Direction

Enriched term with up-regulated (up), down-regulated (down) or both up/down-regulated (all) genes

Method

Enrichment methods. ORA: Over-representation analysis

DB

Ontology database

ID

ID of the enrichment term in the ontology database

Description

Description of the enriched term

GeneRatio

Gene Ratio. See clusterProfiler package for details

BgRatio

Background Ratio. See clusterProfiler package for details

pvalue

p-value

p.adjust

p-values adjusted for multiple testing using "BH" method. See p.adjust for details.

qvalue

p-values adjusted for multiple testing using "qvalue" method. See qvalue package for details.


altintasali/ontoClust documentation built on Dec. 19, 2021, 1:36 a.m.