| genotyping {breakpointR} | R Documentation |
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) genotype.fisher(cReads, wReads, roiReads, background = 0.02, minReads = 10)
breaks |
A |
fragments |
A |
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. |
cReads |
Number of Crick reads. |
wReads |
Number of Watson reads. |
roiReads |
Total number of reads. |
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.
A GRanges-class object with genotyped breakpoint coordinates.
A list with the $bestFit and $pval.
GenotypeBreaks: Genotypes breakpoint defined regions.
genotype.fisher: Assign states to any given region.
David Porubsky, Ashley Sanders, Aaron Taudt
## Get an example file
exampleFolder <- system.file("extdata", "example_results", package="breakpointRdata")
exampleFile <- list.files(exampleFolder, full.names=TRUE)[1]
## Load the file
breakpoint.objects <- get(load(exampleFile))
## Genotype regions between breakpoints
gbreaks <- GenotypeBreaks(breaks=breakpoint.objects$breaks, fragments=breakpoint.objects$fragments)