Description Usage Arguments Details Value Examples

View source: R/getBreakpoints.R

Refine breakpoints with confidence intervals from an initial estimate (from `getBreakpoints`

).

1 2 | ```
refineBreakpoints(model, fragments, breakpoints = model$breakpoints,
confint = 0.99)
``` |

`model` |
An |

`fragments` |
A |

`breakpoints` |
A |

`confint` |
Desired confidence interval for breakpoints. |

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.

An `aneuBiHMM`

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

1 2 3 4 5 6 7 8 9 10 11 12 13 | ```
## 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 Nov. 21, 2018, 10:10 a.m.

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