| 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)