# #——选项,eval = TRUE,回声= FALSE ------------------------------------------- 选项(showHeadLines = 3)选项(showTailLines = 3) # #——设置,包括= FALSE --------------------------------------------------- knitr: opts_chunk美元集(崩溃= TRUE,发表评论 = "#>" ) ## ---- getPackage eval = FALSE --------------------------------------------------- # 如果(!requireNamespace(“BiocManager”,悄悄地= TRUE)) # install.packages (BiocManager) # BiocManager::安装(“VCFArray ") ## ---- getDevel eval = FALSE ----------------------------------------------------- # BiocManager::安装(“Bioconductor / VCFArray ") ## ---- 加载消息= FALSE ------------------------------------------------------ 库(VCFArray) # #——结果,消息= FALSE ----------------------------------------------------- args (VCFArray) fl < -系统。文件(“extdata”、“chr22.vcf.gz”、包=“VariantAnnotation”)图书馆(VariantAnnotation) vcfFields (fl) # #——构造函数 -------------------------------------------------------------- VCFArray(文件= fl, name = " GT ") ## ---- constructor2 ------------------------------------------------------------- vcf < - VariantAnnotation: VcfFile (fl) VCFArray(文件= vcf name = " DS ") ## ---- rgstack ------------------------------------------------------------------ extdata < -系统。file(package =" genome files "， "extdata") files <- dir(extdata, pattern="^CEUtrio. "* bgz美元”,全= TRUE)[1:2](文件)< -子(“名字。* _ ([0-9XY] +)。*"， "\\1"， basename(files)) seqinfo <- as(readRDS(file. txt))路径(extdata seqinfo.rds)),“Seqinfo”)堆栈< - GenomicFiles:: VcfStack(文件、Seqinfo) gr < - (GenomicFiles: Seqinfo(栈)[rownames(栈)],“农庄”)# # RangedVcfStack rgstack < - GenomicFiles:: RangedVcfStack(堆栈,rowRanges = gr) rgstack # #——constructor3 ------------------------------------------------------------- 美元vcfFields (rgstack)基因族群VCFArray (rgstack name = " ") ## ---- 遥远,eval = FALSE ------------------------------------------------------- # chr22url < -“https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz”# chr22url。tbi <- paste0(chr22url， ".tbi") # va <- VCFArray(chr22url, vindex =chr22url。创伤性脑损伤,name = " GT ") ## ---- seedAccessor ------------------------------------------------------------ 弗吉尼亚州< - VCFArray (fl、名称=“GT”)种子(va ) ## ---- vcffileAccessor --------------------------------------------------------- vcffile (va ) ## ---- 会变暗 -------------------------------------------------------------------- va < - VCFArray (fl、名称=“GT”)暗(va)类(dimnames (va)的长度(dimnames (va )) ## ---- 构造子集 -------------------------------------------------------------- 弗吉尼亚州[1:3,1:3) va (c(真的,假的 ), ] ## ---- 数字 ----------------------------------------------------------------- ds < - VCFArray (fl、名称= ds)日志(ds + 5 ) ## ---- VCFArraySeed ------------------------------------------------------------ 种子< - VCFArray::: VCFArraySeed (fl, name =“GT”,pfix = NULL)种子路径(vcffile(种子 )) ## ---- VCFArray-from-VCFArraySeed ---------------------------------------------- ( 弗吉尼亚州< VCFArray(种子 )) ## ---- 达 ---------------------------------------------------------------------- da < - DelayedArray(种子)类(da)所有。平等(da,弗吉尼亚州 ) ## ----------------------------------------------------------------------------- sessionInfo ()