sequenza (version 1.0.5)

find.breaks: Segmentation of sequencing data using an allele-specific copy number algorithm

Description

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

Usage

find.breaks(abf.baf, gamma = 80, kmin = 10, baf.thres = c(0, 0.5), verbose = FALSE, ...)
segment.breaks(abf.tab, breaks)

Arguments

abf.baf

an ABfreq file containing only the heterozygous positions.

abf.tab

a complete ABfreq file.

gamma, kmin, baf.thres, verbose

arguments passed to aspcf.

breaks

breaks as output find.breaks.

...

additional arguments passed to aspcf.

Details

copynumber is a package to perform efficient segmentation of SNP-array data. The function find.breaks uses an allele-specific algorithm 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.

Examples

data.file <-  system.file("data", "abf.data.abfreq.txt.gz", package = "sequenza")
# read all the chromosomes:
abf.data  <- read.abfreq(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:
abf.data  <- read.abfreq(data.file, chr.name = 12)

# Correct the coverage of the loaded chromosome:
abf.data$adjusted.ratio <- abf.data$depth.ratio /
                           gc.vect[as.character(abf.data$GC.percent)]
# Select the heterozygous positions
abf.hom  <- abf.data$ref.zygosity == 'hom'
abf.het  <- abf.data[!abf.hom, ]
# Detect breakpoints
breaks <- find.breaks(abf.het, gamma = 80, kmin = 10, baf.thres = c(0, 0.5))
# use heterozygous and homozygous position to measure segment values
segment.breaks(abf.data, breaks = breaks)