colocalized (version 0.2.0)

chromsearch: Search one chromsome

Description

Search a single chromosome for clusters of TF binding sequences. Example produces a null result, test the same complex on "chr9" for a positive reading.

Usage

chromsearch(choose, n, chrom)

Arguments

choose

List of .bed tables

n

Cut-off distance between colocalized sequences

chrom

Chromosome to be searched given as e.g. "chr19"

Value

A table containing the addresses (as one dimensional intervals) of the members of every cluster, with some annotation data.

Examples

# NOT RUN {
complex<-list(nfkb1,nfkb2,relb)
chromsearch(complex,150,"chrY")
# }