confidenceInterval: Estimate confidence intervals for breakpoints
In breakpointR: Find breakpoints in Strand-seq data

Description Usage Arguments Value Author(s) Examples

Estimate confidence intervals for breakpoints by going outwards from the breakpoint read by read, and multiplying the probability that the read doesn't belong to the assigned segment.

1	confidenceInterval(breaks, fragments, background = 0.05, conf = 0.99)

`breaks`	Genotyped breakpoints as outputted from function `GenotypeBreaks`.
`fragments`	Read fragments from function `readBamFileAsGRanges`.
`background`	The percent (e.g. 0.05 = 5%) of background reads allowed for WW or CC genotype calls.
`conf`	Desired confidence interval of localized breakpoints.

A GRanges-class object of breakpoint ranges for a given confidence interval in conf.

Aaron Taudt, David Porubsky

## Not run:  
## Get an example file 
exampleFolder <- system.file("extdata", "example_results", package="breakpointRdata")
exampleFile <- list.files(exampleFolder, full.names=TRUE)[1]
## Load the file 
breakpoint.objects <- get(load(exampleFile))
## Calculate confidence intervals of genotyped breakpoints
confint <- confidenceInterval(breaks=breakpoint.objects$breaks, fragments=breakpoint.objects$fragments, background=0.02)
## End(Not run)