segmentDensity {nullranges} | R Documentation

## Genome segmentation based on feature density

### Description

This function allows for various methods (see `type`) of segmenting based on the density of features `x`.

### Usage

    segmentDensity(x, n, L_s = 1e+06, exclude = NULL, type = c("cbs", "hmm"))

### Arguments

`x` | the input GRanges, e.g. genes
`n` | the number of states
`L_s` | segment length
`exclude` | GRanges of excluded region
`type` | the type of segmentation, either Circular Binary Segmentation `"cbs"` (which will use 'DNAcopy' to segment) or Hidden Markov Model `"hmm"` (which will use 'RcppHMM'). These packages are not imported by nullranges, but must be installed by the user

### Value

a GRanges with metadata columns containing:

- state segmentation state

- counts average number of genes

### Examples

    n <- 10000
    library(GenomicRanges)
    gr <- GRanges("chr1", IRanges(round(
      c(runif(n/4,1,991), runif(n/4,1001,3991),
        runif(n/4,4001,4991), runif(n/4,7001,9991))),
      width=10), seqlengths=c(chr1=10000))
    gr <- sort(gr)
    exclude <- GRanges("chr1", IRanges(5001,6000), seqlengths=c(chr1=10000))
    seg <- segmentDensity(gr, n=3, L_s=100, exclude=exclude, type="cbs")

[Package nullranges version 1.0.1 Index]