# # - eval = FALSE ------------------------------------------------------------ # 如果(!需要(“BiocManager”))# install.packages (BiocManager) # BiocManager::安装(“RaggedExperiment ") ## ---- 包括= TRUE,结果=“隐藏”,消息= FALSE,警告= FALSE ------------------ 库(RaggedExperiment)库(GenomicRanges ) ## ---- 回声= FALSE, fig.cap = " RaggedExperiment对象示意图。行和列分别表示基因组范围和样本。分析操作可以使用(从左到右)compactAssay, qreduceAssay，和sparseAssay.”，out。宽度= " \ \ maxwidth "——knitr:: include_graphics(“RaggedExperiment.svg ") ## ----------------------------------------------------------------------------- sample1 < -农庄(c(=“chr1:1-10: B =“chr1:8-14: +”,c =“chr2:15-18: +”),得分= 3:5)sample2 < -农庄(c (D =“chr1:1-10: E =“chr2:11-18: +”),分数= 1:2 ) ## ----------------------------------------------------------------------------- colDat < - DataFrame (id = 1:2 ) ## ----------------------------------------------------------------------------- ragexp < - RaggedExperiment (sample1 = sample1 sample2 = sample2 colData = colDat) ragexp ## ----------------------------------------------------------------------------- grl < - GRangesList (sample1 = sample1 sample2 = sample2) RaggedExperiment (grl,colData = colDat ) ## ----------------------------------------------------------------------------- rangeList < -列表(sample1 = sample1 sample2 = sample2) RaggedExperiment (rangeList, colData = colDat ) ## ----------------------------------------------------------------------------- grList < -列表(sample1 = sample1,sample2 = sample2) mcols (grList) < - colDat RaggedExperiment (grList ) ## ----------------------------------------------------------------------------- rowRanges (ragexp ) ## ----------------------------------------------------------------------------- dimnames (ragexp ) ## ----------------------------------------------------------------------------- colData (ragexp ) ## ----------------------------------------------------------------------------- 暗(ragexp)减少(“*”,暗(ragexp)) sparseAssay (ragexp) (sparseAssay (ragexp长度 )) ## ----------------------------------------------------------------------------- sparseAssay (ragexp稀疏= TRUE ) ## ----------------------------------------------------------------------------- compactAssay (ragexp ) ## ----------------------------------------------------------------------------- compactAssay (ragexp稀疏= TRUE ) ## ----------------------------------------------------------------------------- disjoinAssay (ragexpsimplifyDisjoin =意味着 ) ## ----------------------------------------------------------------------------- unlist (grl use.names = FALSE ) ## ----------------------------------------------------------------------------- rowRanges (ragexp)试验(ragexp”分数 ") ## ----------------------------------------------------------------------------- ( 查询< -农庄(c(“chr1:1-14:”,“chr2:11-18 :+"))) ## ----------------------------------------------------------------------------- weightedmean < -函数(分数,范围,qranges) {isects < - pintersect(范围,qranges)和(分数*宽度(isects)) /(宽度(isects求和 )) } ## ----------------------------------------------------------------------------- qreduceAssay (ragexp查询, simplifyReduce = weightedmean) ## ----------------------------------------------------------------------------- library(Matrix) sm <- Matrix::sparseMatrix( i = c(2, 3, 4, 3, 4, 3, 4), j = c(1, 1, 1, 3, 3, 4, 4), x = c(2L, 4L, 2L, 2L, 2L, 4L, 2L), dims = c(4, 4), dimnames = list( c("chr2:1-10", "chr2:2-10", "chr2:3-10", "chr2:4-10"), LETTERS[1:4] ) ) as(sm, "RaggedExperiment") ## ----------------------------------------------------------------------------- sessionInfo()