getSCEcoordinates: Get SCE coordinates

Description Usage Arguments Value Author(s) Examples

View source: R/findSCEs.R

Description

Extracts the coordinates of a sister chromatid exchanges (SCE) from an aneuBiHMM object.

Usage

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getSCEcoordinates(model, resolution = c(3, 6), min.segwidth = 2,
  fragments = NULL)

Arguments

model

An aneuBiHMM object.

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 GRanges-class object with read fragments or a file that contains such an object. These reads will be used for fine mapping of the SCE events.

Value

A GRanges-class object containing the SCE coordinates.

Author(s)

Aaron Taudt

Examples

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## 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)

ataudt/aneufinder documentation built on Nov. 21, 2018, 10:10 a.m.