getBreakpoints {AneuFinder} | R Documentation

## Extract breakpoints

### Description

Extract breakpoints with confidence intervals from an `aneuHMM` or `aneuBiHMM` object.

### Usage

    getBreakpoints(model, fragments = NULL, confint = 0.99)

### Arguments

`model` | An `aneuHMM` or `aneuBiHMM` object or a file that contains such an object.
`fragments` | A `GRanges-class` object with read fragments or a file that contains such an object.
`confint` | Desired confidence interval for breakpoints. Set `confint=NULL` to disable confidence interval estimation.

### Details

Confidence intervals for breakpoints are estimated by going outwards from the breakpoint read by read, and performing a test of getting the observed or a more extreme outcome, given that the reads within the confidence interval belong to the other side of the breakpoint.

### Value

A `GRanges-class` with breakpoint coordinates and confidence interals if `fragments` was specified.

### 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 data into bin size 1Mp
    readfragments <- binReads(bedfile, assembly='mm10', binsize=1e6,
                      chromosomes=c(1:19,'X','Y'), reads.return=TRUE)
    binned <- binReads(bedfile, assembly='mm10', binsize=1e6,
                      chromosomes=c(1:19,'X','Y'))
    ## Fit the Hidden Markov Model
    model <- findCNVs.strandseq(binned[[1]])
    ## Add confidence intervals
    breakpoints <- getBreakpoints(model, readfragments)

[Package AneuFinder version 1.12.1 Index]