calculateSignalToFlankScore: Calculate signal-to-flank score

In ZarnackGroup/BindingSiteFinder: Binding site defintion based on iCLIP data

Calculate signal-to-flank score

Description

This function calculates the signal-to-flank ratio for all present binding sites.

Usage

calculateSignalToFlankScore(
  object,
  flank = c("bs", "manual"),
  flank.size = NULL,
  quiet = FALSE
)

Arguments

object	a BSFDataSet object
flank	character; how the flanking region shoule be set. Options are 'bs', 'manual'
flank.size	numeric; if flank='manual' provide the desired flanking size
quiet	logical; whether to print messages

Details

Each input range is treated as a binding site. For a particular binding site all overlapping crosslinks are summed up and divided by the normalized sum of the crosslinks in the two adjecent regions of the same size. This is done for all bining sites and the ratio is reported as a score.

The function is part of the standard workflow performed by BSFind.

Value

an object of class BSFDataSet with signal-to-flank ratios added to the meta column of the ranges.

See Also

BSFind, bindingSiteDefinednessPlot

Examples

# load clip data
files <- system.file("extdata", package="BindingSiteFinder")
load(list.files(files, pattern = ".rda$", full.names = TRUE))
bds = makeBindingSites(bds, bsSize = 5)
bds = calculateSignalToFlankScore(bds)

ZarnackGroup/BindingSiteFinder documentation built on Nov. 24, 2024, 10:41 a.m.