annotateBreakpoints {AneuFinder} | R Documentation |
Annotate breakpoints as sister-chromatid-exchange (SCE), copy-number-breakpoint (CNB).
annotateBreakpoints(breakpoints)
breakpoints |
A |
The input GRanges-class
with additinal column 'type'.
## 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)