annotateWithScore {BindingSiteFinder} | R Documentation |
This function can be used to annotate a BSFDataSet
object with
merged binding sites with scores from the initial ranges
(eg. PureCLIP scores).
annotateWithScore(object, scoreRanges)
object |
a BSFDataSet object |
scoreRanges |
a GRanges object, with numeric column named 'score' |
an object of class BSFDataSet with updated meta columns of the ranges
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) }