## ------------------------------------------------------------------------ library(hiAnnotator) ## ------------------------------------------------------------------------ data(sites) ## sites object doesn't have a start & stop column to denote genomic range, hence soloStart parameter must be TRUE or a nasty error will be thrown! alldata.rd <- makeGRanges(sites,soloStart=TRUE) data(genes) ## adding freeze populates SeqInfo slot of GRanges object. genes.rd <- makeGRanges(genes, freeze="hg18") ## ----, eval=FALSE-------------------------------------------------------- ## refflat <- getUCSCtable("refFlat","RefSeq Genes") ## genes <- makeGRanges(refflat) ## ------------------------------------------------------------------------ nearestGenes <- getNearestFeature(alldata.rd,genes.rd,"NearestGene") head(nearestGenes) # nearestGenes <- getNearestFeature(alldata.rd,genes.rd,"NearestGene", parallel=TRUE) ## get nearest 5' genes nearestGenes <- getNearestFeature(alldata.rd,genes.rd,"NearestGene",side="5p") head(nearestGenes) ## get nearest 3' genes nearestGenes <- getNearestFeature(alldata.rd,genes.rd,"NearestGene",side="3p") head(nearestGenes) ## get midpoint of genes nearestGenes <- getNearestFeature(alldata.rd,genes.rd,"NearestGene",side="midpoint") head(nearestGenes) ### get two nearest upstream and downstream genes relative the query nearestTwoGenes <- get2NearestFeature(alldata.rd,genes.rd,"NearestGene") head(nearestTwoGenes) ## ------------------------------------------------------------------------ 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)