annotateBreakpoints {AneuFinder} | R Documentation

## Annotate breakpoints

### Description

Annotate breakpoints as sister-chromatid-exchange (SCE), copy-number-breakpoint (CNB).

### Usage

    annotateBreakpoints(breakpoints)

### Arguments

`breakpoints` | A `GRanges-class` as returned by `getBreakpoints`.

### Value

The input `GRanges-class` with additinal column 'type'.

### 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 1.8.0 Index]