refineBreakpoints: Refine breakpoints

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

Refine breakpoints

Description

Refine breakpoints with confidence intervals from an initial estimate (from getBreakpoints).

Usage

refineBreakpoints(model, fragments, breakpoints = model$breakpoints,
  confint = 0.99)

Arguments

model	An aneuBiHMM object or a file that contains such an object.
fragments	A GRanges-class object with read fragments or a file that contains such an object.
breakpoints	A GRanges-class object with breakpoints and confidence intervals, as returned by function getBreakpoints.
confint	Desired confidence interval for breakpoints.

Details

Breakpoints are refined by shifting the breakpoint within its initial confidence interval read by read and maximizing the probability of observing the left-right read distribution.

Value

An aneuBiHMM with adjusted breakpoint coordinates and confidence interals, bins and segments.

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)
## Refine breakpoints
refined.model <- refineBreakpoints(model, readfragments, breakpoints)

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