refineBreakpoints {AneuFinder} | R Documentation |
Refine breakpoints with confidence intervals from an initial estimate (from getBreakpoints
).
refineBreakpoints(model, fragments, breakpoints = model$breakpoints, confint = 0.99)
model |
An |
fragments |
A |
breakpoints |
A |
confint |
Desired confidence interval for breakpoints. |
Breakpoints are refined by shifting the breakpoint within its initial confidence interval read by read and maximizing the probability of observing the left-right read distribution.
An aneuBiHMM
with adjusted breakpoint coordinates and confidence interals, bins and segments.
## 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) ## Refine breakpoints refined.model <- refineBreakpoints(model, readfragments, breakpoints)