breakSeekr: Find breakpoints from deltaWs
In breakpointR: Find breakpoints in Strand-seq data

Description Usage Arguments Value Author(s) Examples

Find breakpoints from deltaWs by localizing significant peaks based on z-score calculation.

1	breakSeekr(deltaWs, trim = 10, peakTh = 0.33, zlim = 3.291)

`deltaWs`	A `GRanges-class` object with metadata column "deltaW" generated by `deltaWCalculator`.
`trim`	The amount of outliers in deltaWs removed to calculate the stdev (10 will remove top 10% and bottom 10% of deltaWs).
`peakTh`	The treshold that the peak deltaWs must pass to be considered a breakpoint (e.g. 0.33 is 1/3 of max(deltaW)).
`zlim`	The number of stdev that the deltaW must pass the peakTh (ensures only significantly higher peaks are considered).

A GRanges-class object containing breakpoint coordinates with various metadata columns.

David Porubsky, Aaron Taudt, Ashley Sanders

## Get an example file 
exampleFolder <- system.file("extdata", "example_bams", package="breakpointRdata")
exampleFile <- list.files(exampleFolder, full.names=TRUE)[1]
## Load the file
fragments <- readBamFileAsGRanges(exampleFile, pairedEndReads=FALSE, chromosomes='chr22')
## Calculate deltaW values
dw <- deltaWCalculator(fragments)
## Get significant peaks in deltaW values
breaks <- breakSeekr(dw)