getBreakpoints {AneuFinder} | R Documentation |
Extract breakpoints with confidence intervals from an aneuHMM
or aneuBiHMM
object.
getBreakpoints(model, fragments = NULL, confint = 0.99)
model |
An |
fragments |
A |
confint |
Desired confidence interval for breakpoints. Set |
Confidence intervals for breakpoints are estimated by going outwards from the breakpoint read by read, and performing a test of getting the observed or a more extreme outcome, given that the reads within the confidence interval belong to the other side of the breakpoint.
A GRanges-class
with breakpoint coordinates and confidence interals if fragments
was specified.
## Get an example BED file with single-cell-sequencing reads bedfile <- system.file("extdata", "KK150311_VI_07.bam.bed.gz", package="AneuFinderData") ## Bin the data into bin size 1Mp readfragments <- binReads(bedfile, assembly='mm10', binsize=1e6, chromosomes=c(1:19,'X','Y'), reads.return=TRUE) binned <- binReads(bedfile, assembly='mm10', binsize=1e6, chromosomes=c(1:19,'X','Y')) ## Fit the Hidden Markov Model model <- findCNVs.strandseq(binned[[1]]) ## Add confidence intervals breakpoints <- getBreakpoints(model, readfragments)