## ----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”）），cache = as.logical（sys.getenv（“knitr_cache”，“true”）），错误= false）## ---- TXDB------------------------------------------------------------------------------------------------- uppressPackageStartUpMessages（{库（“Txdb.rnorvegicus.ucsc。RN5.refgene“）}）TXDB < - TXDB.rnorvegicus.Cucsc.rn5.refgene ##查找所有基因RATGENES < - 基因（TXDB）##列出所有序列SEQINFO（RUTGENES）##子集仅包含标准染色体的标准染色体<- PrecestStandardChromosomes（RATGENES）##找到基因'ACSL5'ACSL5 < - RATGENES [哪个（MCOL（RATGENES）$ GENE_ID == 94340），] ACSL5 ## ---- BSGONOME -------------------------------------------------------------------------------------------------- suppressPackageStartUpMessages（{库（BSGenome.rnorvegicus.ucsc.rn5）}）ratseq < - bsgenome.rnorvegicus.ucc.rn5 class（ratseq）##获取序列ACSL5_Sequence < - GetSeq（Ratseq，ACSL5）##计算GC内容Letterfruency（ACSL5_Sequence，“GC”，As.prob = True）## ----选择-RAT ---------------------------------------------------------------------------------------------------------------------------------------------------------------------论文（“rattus.norvegicus”）##获得所有entrex ID和基因名称之间的映射RatgenEnames < - 选择（rattus.norvegicus，Ratenes $ Gene_ID，列= C（“符号”，'GeneID'），KeyType =“GeneID”）##将entrz ID与子集id id id < - match（ratgenenames $ geneid，Rategenes $ Gene_id）##将碎片状结果添加到Granges MCols（RUTGENES）< - RUTGENENAMES [IDX，] RATGENES ## ---- GTF-TO-GR，EVAL = FALSE --------------------------------------------------------------------------------------＃库（AnnotationHub）#Ah = AnnotationHub（）############-查询（AH，C（“GTF”，“Homo Sapiens”，“grch38","80")) # gtf_humans # # ## download the file # gtfFile <- ah[["AH47066"]] # # ## create a txdb # library(GenomicFeatures) # txdb <- makeTxDbFromGRanges(gtfFile) #may take some time.. # txdb # # ## get the genes from the taxdb object # humanGenes <- genes(txdb) ## ----chainfile------------------------------------------------------------------------------------ ## a) get the chain file ## load the package and query the files to find the file we want library(AnnotationHub) ah = AnnotationHub() query(ah , c("rattus", "rn5", "rn6")) ## learn more about the file you want ah["AH14761"] ## download the file ratChain <- ah[["AH14761"]] ratChain ## b) perform the liftover library(rtracklayer) lft <- liftOver(acsl5, ratChain) lft ## ----sessionInfo---------------------------------------------------------------------------------- sessionInfo()