show,deepSNV-method {deepSNV} | R Documentation

## Show method for deepSNV objects

### Description

Show method for deepSNV objects

### Usage

    ## S4 method for signature 'deepSNV'
    show(object)

### Arguments

`object` | A `deepSNV-class` object.

### Author(s)

Moritz Gerstung

### 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 1.30.0 Index]