deepSNV-package {deepSNV} | R Documentation

## Detection of subclonal SNVs in deep sequencing experiments

### Description

Detection of subclonal SNVs in deep sequencing experiments

### Details

This packages provides algorithms for detecting subclonal single nucleotide variants (SNVs) and their frequencies from ultra-deep sequencing data. It retrieves the nucleotide counts at each position and each strand from two .bam files and tests for differences between the two experiments with a likelihood ratio test using either a binomial or and overdispersed beta-binomial model. The statistic can be tuned across genomic sites by a shared Dirichlet prior and there package provides procedures for normalizing sequencing data from different runs.

### Author(s)

Moritz Gerstung, Wellcome Trust Sanger Institute, moritz.gerstung@sanger.ac.uk

### References

Gerstung M, Beisel C, Rechsteiner M, Wild P, Schraml P, Moch H, and Beerenwinkel N. Reliable detection of subclonal single-nucleotide variants in tumour cell populations. Nat Commun 3:811 (2012). DOI:10.1038/ncomms1814.

### See Also

`deepSNV`

### Examples

    ## Short example with 2 SNVs at frequency ~10%
    regions <- data.frame(chr="B.FR.83.HXB2_LAI_IIIB_BRU_K034", start = 3120, stop=3140)
    ex <- deepSNV(test = system.file("extdata", "test.bam", package="deepSNV"), control = system.file("extdata", "control.bam", package="deepSNV"), regions=regions, q=10)
    show(ex)   # show method
    plot(ex)   # scatter plot
    summary(ex)   # summary with significant SNVs
    ex[1:3,]   # subsetting the first three genomic positions
    tail(test(ex, total=TRUE))   # retrieve the test counts on both strands
    tail(control(ex, total=TRUE))

    ## Not run: Full example with ~ 100 SNVs. Requires an internet connection, but try yourself.
    # regions <- data.frame(chr="B.FR.83.HXB2_LAI_IIIB_BRU_K034", start = 2074, stop=3585)
    # HIVmix <- deepSNV(test = "http://www.bsse.ethz.ch/cbg/software/deepSNV/data/test.bam", control = "http://www.bsse.ethz.ch/cbg/software/deepSNV/data/control.bam", regions=regions, q=10)
    data(HIVmix) # attach data instead..
    show(HIVmix)
    plot(HIVmix)
    head(summary(HIVmix))

[Package deepSNV version 1.33.3 Index]