reproducibiliyCutoffPlot {BindingSiteFinder} | R Documentation |
Plotting function for settings specified in
reproducibilityFilter
.
reproducibiliyCutoffPlot( object, cutoff = 0.05, min.crosslinks = 1, max.range = 20, ... )
object |
a BSFDataSet object |
cutoff |
a vector of length = 1, or of length = levels(meta$conditions) with a single number (between 0-1) indicating the quantile cutoff |
min.crosslinks |
numeric of length = 1, defines the lower boundary for the minimum number of crosslinks a binding site has to be supported by all replicates, regardless of the replicate specific quantile threshold |
max.range |
maximum number of crosslinks per sites that should be shown |
... |
further arguments passed to ggplot |
a plot of type ggplot2
showing the per replicate
reproducibility cutoffs based on a given quantile threshold
# load data files <- system.file("extdata", package="BindingSiteFinder") load(list.files(files, pattern = ".rda$", full.names = TRUE)) # merge binding sites bds <- makeBindingSites(object = bds, bsSize = 9, minWidth = 2, minCrosslinks = 2, minClSites = 1) # use a single quantile cutoff reproducibiliyCutoffPlot(bds, max.range = 20, cutoff = c(0.05)) # use condition specific quantile cutoffs reproducibiliyCutoffPlot(bds, max.range = 20, cutoff = c(0.1, 0.05))