## ----风格，echo = false，结果='Asis'----------------------------------- Biocstyle :: Markdown（CSS.Files = C（'custom.css'））## ---- echo = false ---------------------------------------------------- uppressPackageStartUpMessages（{库（rnamodr）}）## ---- eval = false -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SetClass（class =“examplesequencessataframe”，包含=“SequenceFrame”）exceplesequencessataframe < - 函数（DF，范围，序列，复制，条件，Bamfiles，SeqInfo）{rnamodr :::。SequenceAtaframe（“示例”，df，范围，序列，复制，条件，bamfiles，seqinfo）} setClass（class =“examplesequenceSata”，包含=“sequenceData”，slots = c（Unlistdata =“examplesequenceAtchataframe”），prototype = list（UnlistData = examplesequencessquencessquencessquencessquencess，Unlymartype =“examplesequencesataframe”，Minquality = 5L，DatadeCriction =“示例数据”））考试eSequencesata < - 函数（Bamfiles，Annotation，Sequences，SeqInfo，...）{rnamodr ::: sequenceata（“示例”，Bamfiles = Bamfiles，Annotation = Annotation，Sequences =序列，SEQINFO = SEQINFO，...）}＃＃--------------------------------------------------------------------------------- setMethod（“getdata”，signature = c（x =“examplesequenceata”，bamfiles =“bamfilelist”，grl =“grangeslist”，序列=“xstringeet”，param =“scanbamparam”），定义=函数（x，bamfiles，grl，序列，param，args）{###}）## --------------------------------------------------------------------------------------------- setMethod（“aggregateData”，签名= C（x =“examplesequenceAta”），功能（x，条件= c（“两个”，“治疗“，”，“控制”））{###}）## --------------------------------------------------------------------------------------- setClass("ModExample", contains = c("RNAModifier"), prototype = list(mod = "X", score = "score", dataType = "ExampleSequenceData")) ModExample <- function(x, annotation, sequences, seqinfo, ...){ RNAmodR:::Modifier("ModExample", x = x, annotation = annotation, sequences = sequences, seqinfo = seqinfo, ...) } ## ----------------------------------------------------------------------------- setReplaceMethod(f = "settings", signature = signature(x = "ModExample"), definition = function(x, value){ x <- callNextMethod() # validate special setting here x@settings[names(value)] <- unname(.norm_example_args(value)) x }) ## ----------------------------------------------------------------------------- setMethod(f = "aggregateData", signature = signature(x = "ModExample"), definition = function(x, force = FALSE){ # Some data with element per transcript } ) ## ----------------------------------------------------------------------------- setMethod("findMod", signature = c(x = "ModExample"), function(x){ # an element per modification found. } ) ## ----------------------------------------------------------------------------- setClass("ModSetExample", contains = "ModifierSet", prototype = list(elementType = "ModExample")) ModSetExample <- function(x, annotation, sequences, seqinfo, ...){ RNAmodR:::ModifierSet("ModExample", x = x, annotation = annotation, sequences = sequences, seqinfo = seqinfo, ...) } ## ----------------------------------------------------------------------------- setMethod( f = "getDataTrack", signature = signature(x = "ExampleSequenceData"), definition = function(x, name, ...) { ### } ) setMethod( f = "getDataTrack", signature = signature(x = "ModExample"), definition = function(x, name, type, ...) { } ) setMethod( f = "plotDataByCoord", signature = signature(x = "ModExample", coord = "GRanges"), definition = function(x, coord, type = "score", window.size = 15L, ...) { } ) setMethod( f = "plotData", signature = signature(x = "ModExample"), definition = function(x, name, from, to, type = "score", ...) { } ) setMethod( f = "plotDataByCoord", signature = signature(x = "ModSetExample", coord = "GRanges"), definition = function(x, coord, type = "score", window.size = 15L, ...) { } ) setMethod( f = "plotData", signature = signature(x = "ModSetExample"), definition = function(x, name, from, to, type = "score", ...) { } ) ## ----------------------------------------------------------------------------- sessionInfo()