plotStatistics {wavClusteR} | R Documentation |
Graphical representation of cluster statistics, featuring pairwise correlations in the upper panel.
plotStatistics(clusters, corMethod = 'spearman', lower = panel.smooth, ...)
clusters |
GRanges object containing individual clusters as identified by the getClusters function |
corMethod |
A character defining the correlation coefficient to be
computed. See the help page of the |
lower |
A function compatible with the |
... |
Additional parameters to be passed to the |
called for its effect
Federico Comoglio
require(BSgenome.Hsapiens.UCSC.hg19) data( model, package = "wavClusteR" ) filename <- system.file( "extdata", "example.bam", package = "wavClusteR" ) example <- readSortedBam( filename = filename ) countTable <- getAllSub( example, minCov = 10, cores = 1 ) highConfSub <- getHighConfSub( countTable, supportStart = 0.2, supportEnd = 0.7, substitution = "TC" ) coverage <- coverage( example ) clusters <- getClusters( highConfSub = highConfSub, coverage = coverage, sortedBam = example, method = 'mrn', cores = 1, threshold = 2 ) fclusters <- filterClusters( clusters = clusters, highConfSub = highConfSub, coverage = coverage, model = model, genome = Hsapiens, refBase = 'T', minWidth = 12 ) plotStatistics( clusters = fclusters )