xGSEAconciser: Function to make GSEA results conciser by removing redundant...

In Pi: Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway Level

Description

xGSEAconciser is supposed to make GSEA 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

xGSEAconciser(eGSEA, cutoff = c(0.9, 0.5), verbose = TRUE)

Arguments

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

Note

none

See Also

xGSEAconciser

Examples

RData.location <- "http://galahad.well.ox.ac.uk/bigdata"
## Not run: 
eGSEA_concise <- xGSEAconciser(eGSEA)

## End(Not run)

Pi documentation built on Nov. 26, 2020, 2:01 a.m.