plotSubstitutions {wavClusteR} | R Documentation |
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.
plotSubstitutions(countTable, highlight = "TC", model)
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
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called for its effect
Federico Comoglio and Cem Sievers
filename <- system.file( "extdata", "example.bam", package = "wavClusteR" ) example <- readSortedBam( filename = filename ) countTable <- getAllSub( example, minCov = 10, cores = 1 ) plotSubstitutions(countTable = countTable, highlight = "TC")