annotateWithScore {BindingSiteFinder}

R Documentation

Annotation function for BSFDataSet object

Description

This function can be used to annotate a BSFDataSet object with merged binding sites with scores from the initial ranges (eg. PureCLIP scores).

Usage

annotateWithScore(object, scoreRanges)

Arguments

object	a BSFDataSet object
scoreRanges	a GRanges object, with numeric column named 'score'

Value

an object of class BSFDataSet with updated meta columns of the ranges

Examples

if (.Platform$OS.type != "windows") {
    # load data
    csFile <- system.file("extdata", "PureCLIP_crosslink_sites_example.bed",
                        package="BindingSiteFinder")
    cs = rtracklayer::import(con = csFile, format = "BED")
    clipFiles <- system.file("extdata", package="BindingSiteFinder")
    # two experimental conditions
    meta = data.frame(
    id = c(1,2,3,4),
    condition = factor(c("WT", "WT", "KD", "KD"),
    levels = c("KD", "WT")),
    clPlus = list.files(clipFiles, pattern = "plus.bw$", full.names = TRUE),
    clMinus = list.files(clipFiles, pattern = "minus.bw$",
     full.names = TRUE))
    bds = BSFDataSetFromBigWig(ranges = cs, meta = meta, silent = TRUE)

    # merge binding sites
    bds <- makeBindingSites(object = bds, bsSize = 9, minWidth = 2,
    minCrosslinks = 2, minClSites = 1)

    # annotate with original pureCLIP score
    bdsRe = annotateWithScore(bds, cs)
}

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