annotateBreakpoints: Annotate breakpoints

Description Usage Arguments Value Examples

View source: R/getBreakpoints.R

Description

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

Usage

1
annotateBreakpoints(breakpoints)

Arguments

breakpoints

A GRanges-class as returned by getBreakpoints.

Value

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

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
## 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 Nov. 21, 2018, 10:10 a.m.