confidenceInterval.binomial: Estimate confidence intervals for breakpoints

In breakpointR: Find breakpoints in Strand-seq data

Description

Estimate confidence intervals for breakpoints by going outwards from the breakpoint read by read, and performing a binomial test of getting the observed or a more extreme outcome, given that the reads within the confidence interval belong to the other side of the breakpoint.

Usage

confidenceInterval.binomial(breaks, fragments, background = 0.02, 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.binomial(breakpoint.objects$breaks, breakpoint.objects$fragments, background=0.02)
## End(Not run)

breakpointR documentation built on Nov. 8, 2020, 8:04 p.m.