MIGSAres-setEnrCutoff: Set enrichment cutoff for a MIGSAres object

In MIGSA: Massive and Integrative Gene Set Analysis

Description

setEnrCutoff sets the enrichment cutoff value for a MIGSAres object in order to get detailed enrichment results.

Usage

setEnrCutoff(object, newEnrCutoff)

## S4 method for signature 'MIGSAres,numeric'
setEnrCutoff(object, newEnrCutoff)

Arguments

object	a MIGSAres object.
newEnrCutoff	numeric value in range [0,1] or NA to set the new enrichment cutoff. If NA then enrichment cutoff is unset for object.

Value

A MIGSAres object with the updated slots.

Examples

data(migsaRes)
## After executing MIGSA, the MIGSAres object does not have an enrichment
## cutoff set, so it will be shown as follows:
head(migsaRes)
## Now lets set an enrichment cutoff, and then show again the object.
migsaResWCoff <- setEnrCutoff(migsaRes, 0.01)
head(migsaResWCoff)
## So now we can do stuff like check how many gene sets are enriched in both
## experiments, in each one, etc. Moreover now we can do different MIGSAres
## plots available in MIGSA package.
table(migsaResWCoff[, c("igsaInput1", "igsaInput2")])
## And with different cutoffs.
migsaResWCoff <- setEnrCutoff(migsaRes, 0.1)
table(migsaResWCoff[, c("igsaInput1", "igsaInput2")])

MIGSA documentation built on Nov. 8, 2020, 8:26 p.m.