slidingJaccard: Plot two functional annotation charts using a sliding Jaccard...

In CompGO: An R pipeline for .bed file annotation, comparing GO term enrichment between gene sets and data visualisation

Description

This function compares two functional annotation charts using a sliding Jaccard coefficient - a ranked list of P-values is produced, and a sliding window is used to find the Jaccard coefficient of two charts at different cutoffs of the top n terms. This is useful to determine where the majority of overlapping terms is located, and can also be used to compare Jaccard profiles between multiple (up to 4) sets if C and D are supplied.

Usage

slidingJaccard(setA, setB, increment = 50, setC = NULL, setD = NULL)

Arguments

setA	A DAVIDFunctionalAnnotationChart to compare
setB	A DAVIDFunctionalAnnotationChart to compare
increment	The number of terms (n) to increment for each sliding window
setC	A DAVIDFunctionalAnnotationChart to compare, optional
setD	A DAVIDFunctionalAnnotationChart to compare, optional

Examples

data(funChart1)
data(funChart2)
slidingJaccard(funChart1, funChart2, 50, FALSE)

CompGO documentation built on Nov. 8, 2020, 8:22 p.m.