trainingData {RNAmodR.ML} | R Documentation |
trainingData
subsets the aggregate data of a ModifierML
object
to positions as defined by coord
. Positions with an entry in the
mod
column are labeled TRUE
.
trainingData(x, coord, ...) ## S4 method for signature 'ModifierML,GRanges' trainingData(x, coord, ...) ## S4 method for signature 'ModifierML,GRangesList' trainingData(x, coord, ...)
x |
a |
coord |
a |
... |
See |
a CompressedSplitDataFrameList
with aggregate data and an
addition label column.
For more details have a look at
subsetByCoord
.
data("dmod",package = "RNAmodR.ML") setClass("ModMLExample", contains = c("RNAModifierML"), prototype = list(mod = c("D"), score = "score", dataType = c("PileupSequenceData", "CoverageSequenceData"), mlModel = character(0))) data("me",package = "RNAmodR.ML") nextUPos <- function(gr){ nextU <- lapply(seq.int(1L,2L), function(i){ subseq <- subseq(RNAmodR::sequences(me)[dmod$Parent], start(dmod)+3L) pos <- start(dmod) + 2L + vapply(strsplit(as.character(subseq),""), function(y){which(y == "U")[i]},integer(1)) ans <- dmod ranges(ans) <- IRanges(start = pos, width = 1L) ans }) nextU <- do.call(c,nextU) nextU$mod <- NULL unique(nextU) } nondmod <- nextUPos(dmod) nondmod <- nondmod[!(nondmod %in% dmod)] coord <- unique(c(dmod,nondmod)) coord <- coord[order(as.integer(coord$Parent))] trainingData(me,coord)