Mergeomics (version 1.0.0)

tool.coalesce: Calculate overlaps between groups (main function)

Description

tool.coalesce is utilized to merge and trim either overlapping modules (containing shared genes) or overlapping genes (containing shared markers)

Usage

tool.coalesce(items, groups, rcutoff = 0, ncore = NULL)

Arguments

items

array of item identities

groups

array of group identities for items

rcutoff

maximum overlap not coalesced

ncore

minimum number of items required for trimming

Value

CLUSTER

cluster identities after merging and triming (a subset of group identities)

ITEM

item identities

GROUPS

comma separated overlapping group identities

References

Shu L, Zhao Y, Kurt Z, Byars S, Tukiainen T, Kettunen J, Ripatti S, Zhang B, Inouye M, Makinen VP, Yang X. Mergeomics: integration of diverse genomics resources to identify pathogenic perturbations to biological systems. bioRxiv doi: http://dx.doi.org/10.1101/036012

Examples

## read the coexpr module file as an example:
moddata <- tool.read(system.file("extdata",
"modules.mousecoexpr.liver.human.txt", package="Mergeomics"))

## let us find the overlapping ratio between first 10 modules in the file:
## to merge overlapping modules first collect member genes:
mod.names <- unique(moddata$MODULE)[1:min(length(unique(moddata$MODULE)),
10)]
moddata <- moddata[which(!is.na(match(moddata$MODULE, mod.names))),]

## Merge and trim overlapping modules.(max allowed overlap ratio is 0.33)
rmax <- 0.33
moddata$OVERLAP <- moddata$MODULE
moddata <- tool.coalesce(items=moddata$GENE, groups=moddata$MODULE,
rcutoff=rmax)
moddata$MODULE <- moddata$CLUSTER
moddata$GENE <- moddata$ITEM
moddata$OVERLAP <- moddata$GROUPS
moddata <- moddata[,c("MODULE", "GENE", "OVERLAP")]
moddata <- unique(moddata)