breaks: Segmentation of sequencing data using an allele-specific copy...
In sequenza: Copy Number Estimation from Tumor Genome Sequencing Data

Description Usage Arguments Details Examples

This function uses aspcf or pcf from the package copynumber to segment depth ratio and B-allele frequency obtained from sequencing data.

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find.breaks(seqz.baf, gamma = 80, kmin = 10, baf.thres = c(0, 0.5),
            verbose = FALSE, seg.algo = "aspcf", ...)
segment.breaks(seqz.tab, breaks, min.reads.baf = 1, weighted.mean = TRUE)

`seqz.baf`	an seqz file containing only the heterozygous positions.
`seqz.tab`	a complete seqz file.
`gamma, kmin, baf.thres, verbose`	arguments passed to the segmentation algorithm.
`breaks`	breaks as output by `find.breaks`.
`min.reads.baf`	threshold on the depth of the positions included to calculate the average BAF for segment.
`weighted.mean`	boolean to select if the segments have to calculated using the read depth as a weights to calculate depth ratio and B-allele frequency means.
`seg.algo`	Selects the algorithm used for the segmentation. Available options are `aspcf` of `pcf`.
`...`	additional arguments passed to `aspcf`.

copynumber is a package to perform efficient segmentation of SNP-array data. The function find.breaks uses the algorithms from the copynumber package to find break points, where the default parameters have been optimized for sequencing data, but a careful choice of an optimal gamma value is advised.

  ## Not run: 

data.file <-  system.file("extdata", "example.seqz.txt.gz", package = "sequenza")
# read all the chromosomes:
seqz.data  <- read.seqz(data.file)
# Gather genome wide GC-stats from raw file:
gc.stats <- gc.sample.stats(data.file)
gc.vect  <- setNames(gc.stats$raw.mean, gc.stats$gc.values)
# Read only one chromosome:
seqz.data  <- read.seqz(data.file, chr.name = 12)

# Correct the coverage of the loaded chromosome:
seqz.data$adjusted.ratio <- seqz.data$depth.ratio /
                           gc.vect[as.character(seqz.data$GC.percent)]
# Select the heterozygous positions
seqz.hom  <- seqz.data$zygosity.normal == 'hom'
seqz.het  <- seqz.data[!seqz.hom, ]
# Detect breakpoints
breaks <- find.breaks(seqz.het, gamma = 80, kmin = 10, baf.thres = c(0, 0.5))
# use heterozygous and homozygous position to measure segment values
segment.breaks(seqz.data, breaks = breaks)
   
## End(Not run)