confidenceInterval: Estimate confidence intervals for breakpoints

In daewoooo/breakpointR: Find breakpoints in Strand-seq data

Estimate confidence intervals for breakpoints

Description

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.

Usage

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

Arguments

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.

Value

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

Author(s)

Aaron Taudt, David Porubsky

Examples

## 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)

daewoooo/breakpointR documentation built on April 20, 2023, 4:13 p.m.