wavClusteR (version 2.6.2)

plotSubstitutions: 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

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")