bumphunter (version 1.12.0)

clusterMaker: Make clusters of genomic locations based on distance

Description

Genomic locations are grouped into clusters based on distance: locations that are close to each other are assigned to the same cluster. The operation is performed on each chromosome independently.

Usage

clusterMaker(chr, pos, assumeSorted = FALSE, maxGap = 300)
boundedClusterMaker(chr, pos, assumeSorted = FALSE, maxClusterWidth = 1500, maxGap = 500)

Arguments

chr

A vector representing chromosomes. This is usually a character vector, but may be a factor or an integer.

pos

A numeric vector with genomic locations.

assumeSorted

This is a statement that the function may assume that the vector pos is sorted (within each chr). Allowing the function to make this assumption may increase the speed of the function slightly.

maxGap

An integer. Genomic locations within maxGap from each other are placed into the same cluster.

maxClusterWidth

An integer. A cluster large than this width is broken into subclusters.

Value

A vector of integers to be interpreted as IDs for the clusters, such that two genomic positions with the same cluster ID is in the same cluster. Each genomic position receives one integer ID.

Details

The main purpose of the function is to genomic location into clusters that are close enough to perform operations such as smoothing. A genomic location is a combination of a chromosome (chr) and an integer position (pos). Specifically, genomic intervals are not handled by this function.

Each chromosome is clustered independently from each other. Within each chromosome, clusters are formed in such a way that two positions belong to the same cluster if they are within maxGap of each other.

Examples

N <- 1000
chr <- sample(1:5, N, replace=TRUE)
pos <- round(runif(N, 1, 10^5))
o <- order(chr, pos)
chr <- chr[o]
pos <- pos[o]
regionID <- clusterMaker(chr, pos)
regionID2 <- boundedClusterMaker(chr, pos)