getSCEcoordinates {AneuFinder} | R Documentation

## Get SCE coordinates

### Description

Extracts the coordinates of a sister chromatid exchanges (SCE) from an `aneuBiHMM` object.

### Usage

    getSCEcoordinates(model, resolution = c(3, 6), min.segwidth = 2,
      fragments = NULL)

### Arguments

`model` | An `aneuBiHMM` object.
`resolution` | An integer vector specifying the resolution at bin level at which to scan for SCE events.
`min.segwidth` | Segments below this width will be removed before scanning for SCE events.
`fragments` | A `GRanges-class` object with read fragments or a file that contains such an object. These reads will be used for fine mapping of the SCE events.

### Value

A `GRanges-class` object containing the SCE coordinates.

### Author(s)

Aaron Taudt

### Examples

    ## Get an example BED file with single-cell-sequencing reads
    bedfile <- system.file("extdata", "KK150311_VI_07.bam.bed.gz", package="AneuFinderData")
    ## Bin the BAM file into bin size 1Mp
    binned <- binReads(bedfile, assembly='hg19', binsize=1e6,
                      chromosomes=c(1:22,'X','Y'), pairedEndReads=TRUE)
    ## Fit the Hidden Markov Model
    ## Find copy-numbers
    model <- findCNVs.strandseq(binned[[1]])
    ## Find sister chromatid exchanges
    model$sce <- getSCEcoordinates(model)
    print(model$sce)
    plot(model)

[Package AneuFinder version 1.8.0 Index]