# #——风格,回声= FALSE,结果= '飞机 '-------------------------------------------------------- BiocStyle:减价()选项(宽度= 100,max.print = 1000) knitr:: opts_chunk设置(eval = as.logical (Sys美元。采用“KNITR_EVAL”,“真正的”)),缓存= as.logical (Sys。采用“KNITR_CACHE”,“真正的”)),错误= FALSE) # #——回声= FALSE,消息= FALSE -------------------------------------------------------------------- suppressPackageStartupMessages({库(GenomicRanges)图书馆(GenomicAlignments)图书馆(RNAseqData.HNRNPC.bam.chr14)库(AnnotationHub)库(TxDb.Hsapiens.UCSC.hg19.knownGene)库(org.Hs.eg.db)})啊= AnnotationHub () fa < -啊[[“AH18522”]]# #------------------------------------------------------------------------------------------------- ## 1。加载软件包库(基因组范围)库(基因组对齐)## 2。bf <- BamFile(RNAseqData.HNRNPC.bam. ch14)ch14_bamfiles [[1]]， asMates=TRUE) ## 3。定义我们的“感兴趣的区域”roi <- GRanges(“chr14”，IRanges(19653773, width=1)) ## 4。我们的roi paln <- readGAlignmentsList(bf) j <- summarizejunction (paln, with.revmap=TRUE) j_overlap <- j[j %over% roi] ## 5。支持读取paln[j_overlap$revmap[[1]]] ## ----ahdemo，eval = FALSE --------------------------------------------------------------------------- # 库(AnnotationHub) #啊= AnnotationHub () ## ---- ah2 ------------------------------------------------------------------------------------------ ## 数据可以从下列来源是独一无二的(啊dataprovider美元)# #以下类型的文件 retrieved from the hub unique(ah$sourcetype) ## We will download all _Homo sapiens_ cDNA sequences from the FASTA file ## 'Homo_sapiens.GRCh38.cdna.all.fa' from Ensembl using ## `r Biocpkg("AnnotationHub")`. ah2 <- query(ah, c("fasta", "homo sapiens", "Ensembl")) fa <- ah2[["AH18522"]] fa ## ----gene-model-discovery------------------------------------------------------------------------- library("TxDb.Hsapiens.UCSC.hg19.knownGene") txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene txdb methods(class=class(txdb)) genes(txdb) ## ----select--------------------------------------------------------------------------------------- library(org.Hs.eg.db) select(org.Hs.eg.db, c("BRCA1", "PTEN"), c("ENTREZID", "GENENAME"), "SYMBOL") keytypes(org.Hs.eg.db) columns(org.Hs.eg.db) ## ----sessionInfo---------------------------------------------------------------------------------- sessionInfo()