breakSeekr {breakpointR} | R Documentation |
Find breakpoints from deltaWs by localizing significant peaks based on z-score calculation.
breakSeekr(deltaWs, trim = 10, peakTh = 0.33, zlim = 3.291)
deltaWs |
A |
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)