| setEnrCutoff {MIGSA} | R Documentation |
setEnrCutoff sets the enrichment cutoff value for a MIGSAres object in
order to get detailed enrichment results.
setEnrCutoff(object, newEnrCutoff) ## S4 method for signature 'MIGSAres,numeric' setEnrCutoff(object, newEnrCutoff)
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. |
A MIGSAres object with the updated slots.
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")])