feaResult-class: feaResult object

In signatureSearch: Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

Description

The feaResult object stores Functional Enrichment Analysis (FEA) results generated by the corresponding Target and Drug Set Enrichment methods (here TSEA and DSEA) defined by signatureSearch. This includes slots for the FEA results in tabular format, the organism information, and the type of functional annotation used (e.g. GO or KEGG). It also includes the drug information used for the FEA, as well as the corresponding target protein information.

Slots

result

tibble object, this tabular result contains the enriched functional categories (e.g. GO terms or KEGG pathways) ranked by the corresponding enrichment statistic. The result table can be extracted via the result accessor function.

Description of the columns that are shared among the result tables generated by the different FEA methods:

• ont: in case of GO, one of BP, MF, CC, or ALL

• ID: GO or KEGG IDs

• Description: description of functional category

• p.adjust: p-value adjusted for multiple hypothesis testing based on method specified under pAdjustMethod argument

• qvalue: q value calculated with R's qvalue function to control FDR

• itemID: IDs of items (genes for TSEA, drugs for DSEA) overlapping among test and annotation sets.

• setSize: size of the functional category

organism

organism information of the annotation system. Currently, limited to 'human', since drug-target annotations are too sparse for other organisms.

ontology

ontology type of the GO annotation system. If the annotation system is KEGG, it will be 'KEGG'

drugs

input drug names used for the enrichment test

targets

target information for the query drugs obtained from the chosen drug-target annotation source.

signatureSearch documentation built on April 16, 2021, 6 p.m.