plotSubstitutions {wavClusteR} | R Documentation

## Barplot visualization of the number of genomic positions exhibiting a given substitution and, if model provided, additional diagnostic plots.

### Description

Graphical representation of the total number of genomic positions exhibiting one or more substitutions of a given type. This information is used to estimate the mixing coefficients of the non-parametric mixture model. If the mixture model fit is provided, returns additional diagnostic plots such as the total number of reads exhibiting a given substitution and relative substitution frequency-dependent representations of the total number of genomic positions with substitutions of a given type.

### Usage

    plotSubstitutions(countTable, highlight = "TC", model)

### Arguments

`countTable` | A GRanges object, corresponding to a count table as returned by the getAllSub function
`highlight` | A character indicating which substitution should be highlighted in the barplot. A standard PAR-CLIP experiment employing 4-SU treatment induces T to C transitions, encoded as "TC". Default is "TC".
`model` | A list containing the model as returned by the function `fitMixtureModel`

### Value

called for its effect

### Author(s)

Federico Comoglio and Cem Sievers

### See Also

`getAllSub`

### Examples

    filename <- system.file( "extdata", "example.bam", package = "wavClusteR" )
    example <- readSortedBam( filename = filename )
    countTable <- getAllSub( example, minCov = 10, cores = 1 )
    plotSubstitutions(countTable = countTable, highlight = "TC")

[Package wavClusteR version 2.12.1 Index]