# #——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。## setup, echo=FALSE, messages=FALSE，警告= FALSE -------------------------------------------- suppressPackageStartupMessages({库(AnnotationDbi)图书馆(AnnotationHub)图书馆(GenomicFeatures)图书馆(biomaRt)图书馆(org.Hs.eg.db)库(TxDb.Hsapiens.UCSC.hg19.knownGene ) }) ## ---- 配置测试 -------------------------------------------------------------------------------stopifnot (getRversion () > = ' 3.2 ' & & getRversion () < 3.3, BiocInstaller: biocVersion() = = 3.2” " ) ## ---- gene-model-discovery ------------------------------------------------------------------------- 库(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb < - TxDb.Hsapiens.UCSC.hg19。(类=类(txdb knownGene txdb方法 )) ## ---- txdb-exons ----------------------------------------------------------------------------------- 外显子(txdb) exonsBy (tx txdb。 ") ## ---- bsgenome ------------------------------------------------------------------------------------- < - BSgenome.Hsapiens.UCSC库(BSgenome.Hsapiens.UCSC.hg19)基因组。hg19 getSeq(基因外显子(txdb) [1:10 0 ]) ## ---- org ------------------------------------------------------------------------------------------ 库(org.Hs.eg.db) org.Hs.eg.db # #——选择 --------------------------------------------------------------------------------------- 选择(org.Hs.eg.db, c(“BRCA1”、“PTEN”),c(“ENTREZID”、“GENENAME”),“象征”)keytypes (org.Hs.eg.db)列(org.Hs.eg.db) # #——organismdb ----------------------------------------------------------------------------------- 库(Homo.sapiens)选择(Homo。智人,c(“BRCA1”、“PTEN”),c(“TXNAME”、“TXCHROM”,“TXSTART”、“TXEND”),“象征 ") ## ---- biomart eval = FALSE -------------------------------------------------------------------------- # ## 需要上网! !#库(biomaRt) #头(listMarts(), 3) # #列表集市#头(listDatasets (useMart(“运用”)),3)#运用< - # # # #集市数据集完全指定的集市# useMart(“运用”,数据集=“hsapiens_gene_ensembl”)# #头(listFilters(运用),3)# # #过滤器myFilter < -“chromosome_name”# substr (filterOptions (myFilter运用),1,50) # # # myvalue返回值< - c(“21”、“22”)#头(listAttributes(运用),3)# # # myAttributes < - c(属性“ensembl_gene_id”、“chromosome_name ") # # ## 组装和查询集市# res < - getBM(属性= myAttributes过滤器= myFilter #值= myvalue集市=运用)# #——annotationhub-gtf,eval = FALSE ---------------------------------------------------------------- # 库(AnnotationHub) #中心< - AnnotationHub() # #查询中心(中心,c(“运用”、“80”、“gtf”))# # # ensgtf =显示(中心)#视觉选择#中心(“AH47107”)# gtf < -中心[[“AH47107”]]# gtf # txdb < - GenomicFeatures:: makeTxDbFromGRanges (gtf) # #——annotationhub-orgdb, eval=FALSE-------------------------------------------------------------- # library(AnnotationHub) # hub <- AnnotationHub() # query(hub, "OrgDb") ## ----annotationhub-roadmap, eval=FALSE------------------------------------------------------------ # library(AnnotationHub) # hub <- AnnotationHub() # query(hub , c("EpigenomeRoadMap", "E126", "H3K4ME2")) # E126 <- hub[["AH29817"]] ## ----annotationhub-liftover, eval=FALSE----------------------------------------------------------- # query(hub , c("hg19", "hg38", "chainfile")) # chain <- hub[["AH14150"]] ## ----liftover, eval=FALSE------------------------------------------------------------------------- # library(rtracklayer) # E126hg38 <- liftOver(E126, chain) # E126hg38 ## ----vcf, message=FALSE--------------------------------------------------------------------------- ## input variants library(VariantAnnotation) fl <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation") vcf <- readVcf(fl, "hg19") seqlevels(vcf) <- "chr22" ## known gene model library(TxDb.Hsapiens.UCSC.hg19.knownGene) coding <- locateVariants(rowRanges(vcf), TxDb.Hsapiens.UCSC.hg19.knownGene, CodingVariants()) head(coding) ## ----sessionInfo---------------------------------------------------------------------------------- sessionInfo()