genotyping: Set of functions to genotype regions in between localized...
In breakpointR: Find breakpoints in Strand-seq data

Description Usage Arguments Details Value Functions Author(s) Examples

Each defined region is given one of the three states ('ww', 'cc' or 'wc') Consecutive regions with the same state are collapsed

GenotypeBreaks(
  breaks,
  fragments,
  background = 0.05,
  minReads = 10,
  genoT = "fisher"
)

`breaks`	A `GRanges-class` object with breakpoint coordinates.
`fragments`	A `GRanges-class` object with read fragments.
`background`	The percent (e.g. 0.05 = 5%) of background reads allowed for WW or CC genotype calls.
`minReads`	The minimal number of reads between two breaks required for genotyping.
`genoT`	A method ('fisher' or 'binom') to genotype regions defined by a set of breakpoints.

Function GenotypeBreaks exports states of each region defined by breakpoints. Function genotype.fisher assigns states to each region based on expected counts of Watson and Crick reads. Function genotype.binom assigns states to each region based on expected counts of Watson and Crick reads.

A GRanges-class object with genotyped breakpoint coordinates.

GenotypeBreaks: Genotypes breakpoint defined regions.

David Porubsky, Ashley Sanders, Aaron Taudt

## 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))
## Genotype regions between breakpoints
gbreaks <- GenotypeBreaks(breaks=breakpoint.objects$breaks, fragments=breakpoint.objects$fragments)