## ----------------------------------------------------------------------------------------------------------------------------------库（Hiannotator）## -----------------------------------------------------------------------------------------------------------------------------------------数据（站点）##站点对象没有启动和停止列来表示基因组范围，因此Solostart参数必须是真实的，或者将丢弃错误的错误！alldata.rd < - makegranges（sites，solostart = true，freeze =“ hg18”）data（genes）##添加freeze pofulze of Granges对象的seqinfo插槽。genes.rd < - makegranges（基因，冻结=“ hg18”）## ------------------------------------------------------------------------------------------------------------------------------------------------------- # refflat <- getUCSCtable("refFlat", "RefSeq Genes") #基因< - makegranges（refflat）## ----------------------------------------------------------------------------------------------------------------------------------- nearestGenes <- getNearestFeature(alldata.rd, genes.rd, "近距离”）＃最近基因<-getNeareStFeature（alldata.rd，genes.rd，ofkatgene rd，“ ofgearne”，parallel = trual = true）## get feet最近5'get of of of of of genes <-getNeareStFeature（alldata.rd，alldata.rd，genes.rd，genes.rd，''近距离”，side =“ 5p”）头（最近属）##获取最近的3'基因oktergenes <-getNeareStFeature（alldata.rd，genes.rd，genes.rd，'oktergene''，offeratgene'，side =“ 3p”）head（最近基因）## get get get get get get get get get get get get get get get get基因的中点最近基因< - getNeareStFeature（alldata.rd，genes.rd，'seartsgene'，side =“ midpoint”）头（最近属）###获得两个最近的上游基因，相对Query Query Query最近Twogenes最近Twogenes <-get2neareStfeature（Alldata）。RD，Genes.rd，“最近的基因”）头（最近的Twogenes）## ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- geneCounts <- getFeatureCounts(alldata.rd, genes.rd, "NumOfGene") head(geneCounts) # geneCounts <- getFeatureCounts(alldata.rd, genes.rd, "NumOfGene", parallel=TRUE) ## ---- eval=FALSE, echo=TRUE--------------------------------------------------- # geneCounts <- getFeatureCounts(alldata.rd, genes.rd, "NumOfGene", # doInChunks = TRUE, chunkSize = 100) # head(geneCounts) # # geneCounts <- getFeatureCountsBig(alldata.rd, genes.rd, "NumOfGene") # head(geneCounts) ## ----------------------------------------------------------------------------- ## Shows which feature(s) a position was found in. InGenes <- getSitesInFeature(alldata.rd, genes.rd, "InGene") head(InGenes) ## Simply shows TRUE/FALSE InGenes <- getSitesInFeature(alldata.rd, genes.rd, "InGene", asBool = TRUE) head(InGenes) # InGenes <- getSitesInFeature(alldata.rd, genes.rd, "InGene", asBool=TRUE, parallel=TRUE) ## ---- eval=FALSE, echo=TRUE--------------------------------------------------- # doAnnotation(annotType = "within", alldata.rd, genes.rd, "InGene") # doAnnotation(annotType = "counts", alldata.rd, genes.rd, "NumOfGene") # doAnnotation(annotType = "countsBig", alldata.rd, genes.rd, "ChipSeqCounts") # doAnnotation(annotType = "nearest", alldata.rd, genes.rd, "NearestGene") # doAnnotation(annotType = "twoNearest", alldata.rd, genes.rd, "TwoNearestGenes") # geneCheck <- function(x, wanted) { x$isWantedGene <- x$InGene %in% wanted; # return(x) } # doAnnotation(annotType = "within", alldata.rd, genes.rd, "InGene", # postProcessFun = geneCheck, # postProcessFunArgs = list("wanted" = c("FOXJ3", "SEPT9", "RPTOR")) ) ## ---- eval=TRUE, echo=TRUE---------------------------------------------------- res <- doAnnotation(annotType = "within", alldata.rd, genes.rd, "InGene", asBool = TRUE) plotdisFeature(res, "virus", "InGene") res <- doAnnotation(annotType = "nearest", alldata.rd, genes.rd, "NearestGene", side = '5p') plotdisFeature(res, "virus", "X5pNearestGeneDist") data(sites.ctrl) sites$type <- "expr" sites <- rbind(sites,sites.ctrl) alldata.rd <- makeGRanges(sites, soloStart = TRUE) res <- doAnnotation(annotType = "within", alldata.rd, genes.rd, "InGene", asBool = TRUE) plotdisFeature(res, "virus", "InGene") plotdisFeature(res, "virus", "InGene", typeRatio = TRUE) ## ----par_examples, eval=FALSE, echo=TRUE-------------------------------------- # ## Example 1: library(doSMP) # w <- startWorkers(2) # registerDoSMP(w) # getNearestFeature(..., parallel = TRUE) # # ## Example 2: library(doMC) # registerDoMC(2) # getNearestFeature(..., parallel = TRUE) # # ## Example 3: library(doSNOW) # cl <- makeCluster(2, type = "SOCK") # registerDoSNOW(cl) # getNearestFeature(..., parallel = TRUE) # # ## Example 4: library(doParallel) # cl <- makeCluster(2) # registerDoParallel(cl) # getNearestFeature(..., parallel = TRUE)