View source: R/confidenceInterval.R

confidenceInterval.binomial | R Documentation |

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.

```
confidenceInterval.binomial(breaks, fragments, background = 0.02, conf = 0.99)
```

`breaks` |
Genotyped breakpoints as outputted from function |

`fragments` |
Read fragments from function |

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

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