## ----风格，echo = false，结果='Asis'-----------------------------------------------------生物焦质:: markdown（）选项（width = 100，max.print = 1000）knitr :: opts_chunk $ set（eval =as.logical（sys.getenv（“knitr_eval”，“true”）），缓存= as.logical（sys.getenv（“knitr_cache”，“true”）），错误= false）## ---- echo =假，消息=假------------------------------------------------------------- suppressPackageStartArtupMessages（{库（基因组）库（基因组）库（'rnaseqdata.hnrnpc.bam.chr14'）库（注释声）库（“txdb.hsapiens.ucsc.hg19.knowngene”）库（org.hs.eg.db）}）ah = annotationhub（）fa < - ah [[“ah18522”]] ## ----------------------------------------------------------------------------------------------------------加载软件包库（Genomicranges）库（基因组）## 2.加载样本数据库（'rnaseqdata.hnrnpc.bam.chr14'）bf < - bamfile（rnaseqdata.hnrnpc.bam.chr14_bamfiles [[1]]，asmates = true）## 3。定义我们的区域TEREST'ROI < - GRANGES（“CHR14”，讽刺（19653773，宽度= 1））## 4.对齐，结，重叠我们的ROI PALN < - ReadgalignmentsList（BF）J < - SummarizeJunctions（Paln，with.revmap = true）J_OVERLAP < - J [J％OVER％ROI] ## 5.支持读PALN [J_OVERLAP $ REVMAP [[1]]] ## ---- AHDEMO，EVAL = FALSS ----------------------------------------------------------------------------------------＃库（AnnotationHub）＃AH = AnnotationHub（）## ---- AH2 ------------------------------------------------------------------------------------------------------ ##数据来自以下源唯一（ah $ dataprovider）##可以从集线器中检索以下类型的文件 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()