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)