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\name{tool.coalesce.find}
\alias{tool.coalesce.find}
\title{
Find overlapping clusters
}
\description{
\code{tool.coalesce.find} finds overlapped clusters of the given
\code{data} according to a given overlapping ratio by using
\code{\link{tool.overlap}} and \code{\link{tool.cluster}}, respectively. }
\usage{
tool.coalesce.find(data, rmax)
}
\arguments{
\item{data}{a list including ITEM identities and their GROUP identities}
\item{rmax}{maximum overlap not coalesced}
}
\value{data list including clustering results and following components:
\item{CLUSTER }{cluster label}
\item{NODE }{item (node) name}
}
\examples{
## Generate item and group labels for 100 items:
## Assume that unique gene number (items) is 60:
members <- 1:100 ## will be updated
modules <- 1:100 ## will be updated
set.seed(1)
for (i in 1:10){
## each time pick 10 items (genes) from 60 unique item labels
members[(i*10-9):(i*10)] <- sample(60,10)
}
## Assume that unique group labels is 30:
for (i in 1:10){
## each time pick 10 items (genes) from 30 unique group labels
modules[(i*10-9):(i*10)] <- sample(30, 10)
}
rcutoff <- 0.33
ncore <- length(members)
## Default output.
res <- data.frame(CLUSTER=modules, GROUPS=modules, ITEM=members,
stringsAsFactors=FALSE)
## Iterative merging and trimming.
res$COUNT <- 0.0
while(TRUE) {
clust <- tool.coalesce.find(res, rcutoff)
if(is.null(clust)) break
res <- tool.coalesce.merge(clust, ncore)
}
}
\references{
Shu L, Zhao Y, Kurt Z, Byars SG, Tukiainen T, Kettunen J, Orozco LD,
Pellegrini M, Lusis AJ, Ripatti S, Zhang B, Inouye M, Makinen V-P, Yang X.
Mergeomics: multidimensional data integration to identify pathogenic
perturbations to biological systems. BMC genomics. 2016;17(1):874.
}
\author{
Ville-Petteri Makinen
}
|
