pureClipGlobalFilter: Filter PureCLIP sites by their score distribution

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

Filter PureCLIP sites by their score distribution

Description

Function that applies a filter on the global crosslink site score distribution. The GenomicRanges contained in the BSFDataSet need to have a meta-column that holds a numeric score value, which is used for filtering. The name of the column can be set with match.score.

Usage

pureClipGlobalFilter(
  object,
  cutoff = 0.01,
  match.score = "score",
  quiet = FALSE
)

Arguments

object	a BSFDataSet object with stored crosslink ranges of width=1
cutoff	numeric; defines the cutoff for which sites to keep, the smallest step is 1% (0.01)
match.score	character; meta column name of the crosslink site GenomicRanges object that holds the score which is used for sub-setting
quiet	logical; whether to print messages

Details

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

Value

an object of class BSFDataSet with its ranges filtered by those that passed the threshold set with cutoff

See Also

BSFind, pureClipGlobalFilterPlot

Examples

# load data
files <- system.file("extdata", package="BindingSiteFinder")
load(list.files(files, pattern = ".rda$", full.names = TRUE))
# apply 5% filter
pureClipGlobalFilter(object = bds, cutoff = 0.05)

ZarnackGroup/BindingSiteFinder documentation built on April 14, 2025, 1:56 p.m.