colocalized {colocalized}

Colocalized cluster search.

Description

Searches for clusters of colocalized transcription factor (TF) binding sequences. colocalized(choose,chr,n) searches for instances where the sequences from each table element in choose are colocalized to within a cut-off distance.

Usage

colocalized(choose, chr, n, cores)

Arguments

choose

List of .bed tables

chr

Chromosome

n

The cut-off distance

cores

Number of cores for parallel processing. Leaving this blank causes the program to use default (series) processing

Value

Table of clusters found in chr

Examples

complex<-list(nfkb1,nfkb2,relb)
colocalized(complex,"chrY",150)