getSCEcoordinates {AneuFinder} | R Documentation |
Extracts the coordinates of a sister chromatid exchanges (SCE) from an aneuBiHMM
object.
getSCEcoordinates(model, resolution = c(3, 6), min.segwidth = 2, fragments = NULL)
model |
An |
resolution |
An integer vector specifying the resolution at bin level at which to scan for SCE events. |
min.segwidth |
Segments below this width will be removed before scanning for SCE events. |
fragments |
A |
A GRanges-class
object containing the SCE coordinates.
Aaron Taudt
## Get an example BED file with single-cell-sequencing reads bedfile <- system.file("extdata", "KK150311_VI_07.bam.bed.gz", package="AneuFinderData") ## Bin the BAM file into bin size 1Mp binned <- binReads(bedfile, assembly='hg19', binsize=1e6, chromosomes=c(1:22,'X','Y'), pairedEndReads=TRUE) ## Fit the Hidden Markov Model ## Find copy-numbers model <- findCNVs.strandseq(binned[[1]]) ## Find sister chromatid exchanges model$sce <- getSCEcoordinates(model) print(model$sce) plot(model)