xEnrichConciser: Function to make enrichment results conciser by removing...

In hfang-bristol/XGR: Exploring Genomic Relations for Enhanced Interpretation Through Enrichment, Similarity, Network and Annotation Analysis

Function to make enrichment results conciser by removing redundant terms

Description

xEnrichConciser is supposed to make enrichment results conciser by removing redundant terms. A redundant term (called 'B') is claimed if its overlapped part (A&B) with a more significant term (called 'A') meets both criteria: 1) |A&B| > 0.9*|B|; and 2) |A&B| > 0.5*|A|.

Usage

xEnrichConciser(eTerm, cutoff = c(0.9, 0.5), verbose = T)

Arguments

eTerm	an object of class "eTerm"
cutoff	a cutoff vector used to remove redundant terms. By default, it has the first element 0.9 and the second element 0.5. It means, for a term (less significant; called 'B'), if there is a more significant term (called 'A'), their overlapped members cover at least 90 this term B will be defined as redundant and thus being removed
verbose	logical to indicate whether the messages will be displayed in the screen. By default, it sets to false for no display

Value

an object of class "eTerm", after redundant terms being removed.

Note

none

See Also

xEnricherGenes, xEnricherSNPs

Examples

## Not run: 
eTerm_concise <- xEnrichConciser(eTerm)

## End(Not run)

hfang-bristol/XGR documentation built on Feb. 4, 2023, 7:05 a.m.