tool.overlap {Mergeomics} | R Documentation |
tool.overlap
checks each pair of blocks, finds number of shared
items, and obtains significance values of the sharings for block pairs.
tool.overlap(items, groups, nbackground = NULL)
items |
array of item identities |
groups |
array of group identities for items |
nbackground |
total number of items |
a data list including following components
A |
group name |
B |
group name |
POSa |
group name rank |
POSb |
group name rank |
Na |
group A size |
Nb |
group B size |
Nab |
shared items |
R |
overlap ratio |
F |
fold change to null expectation |
P |
overlap P-value (Fisher's test) |
Ville-Petteri Makinen
## 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 two modules: ## pick the first and last modules: mod.names <- unique(moddata$MODULE)[c(1,length(unique(moddata$MODULE)))] if(length(mod.names) > 0){ modA.members <- moddata[which(moddata$MODULE == mod.names[1]),] modB.members <- moddata[which(moddata$MODULE == mod.names[2]),] } mod.pool <- rbind(modA.members, modB.members) overlap.stats <- tool.overlap(mod.pool[,2], mod.pool[,1])