## ----------------------------------------------------------------------------- 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, freeze = "hg18") 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)