annotateBreakpoints: Annotate breakpoints

In ataudt/aneufinder: Analysis of Copy Number Variation in Single-Cell-Sequencing Data

Annotate breakpoints

Description

Annotate breakpoints as sister-chromatid-exchange (SCE), copy-number-breakpoint (CNB).

Usage

annotateBreakpoints(breakpoints)

Arguments

breakpoints

A GRanges-class as returned by getBreakpoints.

Value

The input GRanges-class with additinal column 'type'.

Examples

## 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)

ataudt/aneufinder documentation built on April 18, 2023, 4:20 a.m.