supportRatio {BindingSiteFinder} | R Documentation |
Functions that computes a ratio to determine how well a given binding site
with is supported by the crosslink coverage of the data. For a given
BSFDataSet
object binding sites are computed for each width indicated
in the bsWidths
vector (using the coverageOverRanges
function). These coverages are compared to the coverage of regions flanking
the binding sites. If not indicated in bsFlank
these regions are of
the same width as the binding sites.
supportRatio(object, bsWidths, bsFlank = NA, ...)
object |
a BSFDataSet object |
bsWidths |
a numeric vector indicating the different binding site width to compute the ratio for |
bsFlank |
optional; a numeric vector of the same length as
|
... |
further arguments passed to |
Testing the width of 3nt for example, would result in a coverage within all 3nt wide binding sites (c1) and a coverage computed on the adjacent 3nt flanking the binding sites up- and downstream (f1, f2). Based on these numbers the ratio is computed by: c1/(1/2(f1+f2)).
The median over all ratios is reported as representative value.
an object of class data.frame
# load data files <- system.file("extdata", package="BindingSiteFinder") load(list.files(files, pattern = ".rda$", full.names = TRUE)) supportRatio(bds, bsWidths = c(3,7))