## ----样式，eval = true，echo = false，结果='asis'---------------------------------------选项（Max.print= 1000）biocStyle :: lastx（）库（knitr）opts_chunk $ set（cache = true，tidy = false）##）## ----软件包，eval = true，echo = echo = false，harning = false，message，message = false---------抑制PackagestArtupMessages（{library（shortread）library（variantannotation）库（Parallel）; options（mc.cores = detectcores（））library（ggplot2）library（rnaseqdata.hnrnpc.bam.bam.bam.chr14）library（org.hs）库（org.hs）。-------------------------------------------------------------------------------------ENSIDS <-C（“ ENSG00000130720”，“ ENSG00000103257”，“ ENSG00000156414”，“ ENSG000001444644”，“ ENSG00000159307”，“ ENSG000001444444485”）------------------------------------------------------------------------------------库（org.hs.eg.db）keytypes（org.hs.eg.db）列（org.hs.eg.db）cols <-c（“符号”，“ genEname”）select（org.hs.eg.db，键= endids，列= cols，keytype =“ emembl”）## ----------------------------------------------------------------------------------------------------------- ## ##需要互联网访问！## library（biomart）## head（listmarts（），3）##列表the marts ## head（listDataSets（usemart（usemart（“ emembl”））），3）## mart数据集## emembl <- ##完全指定mart ## usemart（“ emembl”，dataSet =“ hsapiens_gene_ensembl”）## ## head（listFilters（ensembl），3）##滤波器## myfilter <--“ chromosome_name”3）##返回值## myValues <-c（“ 21”，“ 22”）## head（listAttributes（emembl），3）##属性## myattributes <-c（“ emsembl_gene_id”，“ chromosome_name”）## ## ##召集和查询the mart ## res <-getBm（attributes = myAttributes，efferters = myFilter，## valuts = myValues，myvalues，mart = ensembl）## --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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")