## ----style, eval=TRUE, echo=FALSE, results='asis'------------------------ options(max.print=1000) BiocStyle::latex() library(knitr) opts_chunk$set(cache=TRUE, tidy=FALSE) ## ----packages, eval=TRUE, echo=FALSE, warning=FALSE, message=FALSE------- suppressPackageStartupMessages({ library(ShortRead) library(VariantAnnotation) library(parallel); options(mc.cores=detectCores()) library(ggplot2) library(RNAseqData.HNRNPC.bam.chr14) library(org.Hs.eg.db) library(TxDb.Hsapiens.UCSC.hg19.knownGene) library(BSgenome.Hsapiens.UCSC.hg19) library(AnnotationHub) library(rtracklayer) }) ## ----select-setup-------------------------------------------------------- ensids <- c("ENSG00000130720", "ENSG00000103257", "ENSG00000156414", "ENSG00000144644", "ENSG00000159307", "ENSG00000144485") ## ----select-------------------------------------------------------------- library(org.Hs.eg.db) keytypes(org.Hs.eg.db) columns(org.Hs.eg.db) cols <- c("SYMBOL", "GENENAME") select(org.Hs.eg.db, keys=ensids, columns=cols, keytype="ENSEMBL") ## ----biomaRt1, eval=FALSE, results="hide"-------------------------------- ## ## NEEDS INTERNET ACCESS !! ## library(biomaRt) ## head(listMarts(), 3) ## list the marts ## head(listDatasets(useMart("ensembl")), 3) ## mart datasets ## ensembl <- ## fully specified mart ## useMart("ensembl", dataset = "hsapiens_gene_ensembl") ## ## head(listFilters(ensembl), 3) ## filters ## myFilter <- "chromosome_name" ## head(filterOptions(myFilter, ensembl), 3) ## return values ## myValues <- c("21", "22") ## head(listAttributes(ensembl), 3) ## attributes ## myAttributes <- c("ensembl_gene_id","chromosome_name") ## ## ## assemble and query the mart ## res <- getBM(attributes = myAttributes, filters = myFilter, ## values = myValues, mart = ensembl) ## ----rtracklayer-roi----------------------------------------------------- roi <- GRanges("chr10", IRanges(92106877, 112106876, names="ENSG00000099194")) ## ----rtracklayer-session------------------------------------------------- library(rtracklayer) session <- browserSession() ## ----rtracklayer-marks--------------------------------------------------- trackName <- "wgEncodeRegTfbsClusteredV2" tableName <- "wgEncodeRegTfbsClusteredV2" trFactor <- "ERalpha_a" ucscTable <- getTable(ucscTableQuery(session, track=trackName, range=roi, table=tableName, name=trFactor)) ## ----rtracklayer-plot, fig.height=3-------------------------------------- plot(score ~ chromStart, ucscTable, pch="+") abline(v=start(roi) + (end(roi) - start(roi) + 1) / 2, col="blue")