refineBreakpoints {AneuFinder} | R Documentation

## Refine breakpoints

### Description

Refine breakpoints with confidence intervals from an initial estimate (from `getBreakpoints`).

### Usage

    refineBreakpoints(model, fragments, breakpoints = model$breakpoints,
      confint = 0.99)

### Arguments

`model` | An `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.
`breakpoints` | A `GRanges-class` object with breakpoints and confidence intervals, as returned by function `getBreakpoints`.
`confint` | Desired confidence interval for breakpoints.

### Details

Breakpoints are refined by shifting the breakpoint within its initial confidence interval read by read and maximizing the probability of observing the left-right read distribution.

### Value

An `aneuBiHMM` with adjusted breakpoint coordinates and confidence interals, bins and segments.

### 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)
    ## Refine breakpoints
    refined.model <- refineBreakpoints(model, readfragments, breakpoints)

[Package AneuFinder version 1.20.0 Index]