# #——风格,回声= FALSE,结果= '飞机 '------------------------------------ BiocStyle::减价(css。= c(“custom.css文件 ')) ## ---- 回声= FALSE -------------------------------------------------------------- suppressPackageStartupMessages({库(RNAmodR ) }) ## ---- eval = FALSE -------------------------------------------------------------- # 库(RNAmodR ) ## ----------------------------------------------------------------------------- setClass (Class = " ExampleSequenceDataFrame”,包含=“SequenceDFrame”)ExampleSequenceDataFrame < -函数(df、范围、序列、复制条件,{RNAmodR:::。SequenceDataFrame("Example"，df, ranges, sequence, replication, condition, bamfiles, seqinfo)} setClass(Class = "ExampleSequenceData"， contains = "SequenceData"， slots = c(unlistData = "ExampleSequenceDataFrame")， prototype = list(unlistData = "ExampleSequenceDataFrame ()， unlistType = "ExampleSequenceDataFrame"， minQuality = 5L, dataDescription = "Example data")) ExampleSequenceData <- function(bamfiles, annotation, sequences, seqinfo，…){RNAmodR:::SequenceData("Example"， bamfiles = bamfiles，注释=注释,序列=序列,seqinfo = seqinfo , ...) } ## ----------------------------------------------------------------------------- setMethod(“getData”,签名= c (x =“ExampleSequenceData bamfiles =“BamFileList grl =“GRangesList”序列=“XStringSet”,参数=“ScanBamParam”),定义= function (x, bamfiles grl、序列参数,参数 ){ ### } ) ## ----------------------------------------------------------------------------- setMethod(“aggregateData”,签名= c (x = " ExampleSequenceData”),函数(x,条件= c(“两个”,“治疗”,“控制 ")){ ### } ) ## ----------------------------------------------------------------------------- setClass(“ModExample”,包含= c(“RNAModifier”),原型=列表(mod = " X ",得分=“分数”,数据类型=“ExampleSequenceData”))ModExample < -函数(X,注释,序列、seqinfo…){RNAmodR:::修饰符(“ModExample”,X = X,注释=注释,=序列,序列seqinfo = seqinfo,...) } ## ----------------------------------------------------------------------------- setReplaceMethod (f =“设置”,签名=签名(x =“ModExample”),定义= x (x,价值){函数< - callNextMethod() #验证特殊设置这里x@settings[名称(值)]< - unname (.norm_example_args(值))x }) ## ----------------------------------------------------------------------------- setMethod (f =“aggregateData”,签名=签名(x =“ModExample”),定义= function (x,力= FALSE){#每记录一些数据元素 } ) ## ----------------------------------------------------------------------------- setMethod(“findMod”,签名= c (x =“ModExample”)、功能(x){#每修改一个元素。} ) ## ----------------------------------------------------------------------------- setClass(“ModSetExample”,包含=“ModifierSet”,原型=列表(应用=“ModExample”))ModSetExample < -函数(x,注释,序列、seqinfo…){RNAmodR::: ModifierSet(“ModExample”,x = x,注释=注释,=序列,序列seqinfo = seqinfo , ...) } ## ----------------------------------------------------------------------------- setMethod (f = " getDataTrack ",signature = signature(x = "ExampleSequenceData")， definition = function(x, name，…){###})setMethod(f = "getDataTrack"， signature = signature(x, name，…)，definition = function(x, name, type，…){})setMethod(f = "plotDataByCoord"， signature = signature(x = "ModExample"， coord = "GRanges")， definition = function(x, coord, type = "score"，窗口。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"，窗口。尺寸l = 15 , ...) { } ) setMethod (f =“plotData”,签名=签名(x =“ModSetExample”),定义= function (x)的名字,,,type = "分数 ", ...) { } ) ## ----------------------------------------------------------------------------- sessionInfo ()