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, genoT = "fisher") genotype.fisher(cReads, wReads, roiReads, background = 0.05, minReads = 10) genotype.binom(wReads, cReads, background = 0.05, minReads = 10, log = FALSE)
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. |
genoT |
A method ('fisher' or 'binom') to genotype regions defined by a set of breakpoints. |
cReads |
Number of Crick reads. |
wReads |
Number of Watson reads. |
roiReads |
Total number of Crick and Watson reads. |
log |
Set to |
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.
A list
with the $bestFit and $pval.
A list
with the $bestFit and $pval.
GenotypeBreaks
: Genotypes breakpoint defined regions.
genotype.fisher
: Assign states to any given region.
genotype.binom
: Assign states to any given region.
David Porubsky, Ashley Sanders, Aaron Taudt
David Porubsky, Aaron Taudt
David Porubsky
## Get an example file exampleFolder <- system.file("extdata", "example_results", package="breakpointRdata") exampleFile <- list.files(exampleFolder, full.names=TRUE)[1] ## Load the file breakpoint.objects <- get(load(exampleFile)) ## Genotype regions between breakpoints gbreaks <- GenotypeBreaks(breaks=breakpoint.objects$breaks, fragments=breakpoint.objects$fragments)