## ----options, eval=TRUE, echo=FALSE---------------------------------------- options(showHeadLines=3) options(showTailLines=3) ## ----setup, include = FALSE------------------------------------------------ knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----getPackage, eval=FALSE------------------------------------------------ # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("VCFArray") ## ----getDevel, eval=FALSE-------------------------------------------------- # BiocManager::install("Bioconductor/VCFArray") ## ----Load, message=FALSE--------------------------------------------------- library(VCFArray) ## ----avail, message=FALSE-------------------------------------------------- args(VCFArray) fl <- system.file("extdata", "chr22.vcf.gz", package = "VariantAnnotation") library(VariantAnnotation) vcfFields(fl) ## ----constructor----------------------------------------------------------- VCFArray(file = fl, name = "GT") ## ----constructor2---------------------------------------------------------- vcf <- VariantAnnotation::VcfFile(fl) VCFArray(file = vcf, name = "DS") ## ----rgstack--------------------------------------------------------------- extdata <- system.file(package = "GenomicFiles", "extdata") files <- dir(extdata, pattern="^CEUtrio.*bgz$", full=TRUE)[1:2] names(files) <- sub(".*_([0-9XY]+).*", "\\1", basename(files)) seqinfo <- as(readRDS(file.path(extdata, "seqinfo.rds")), "Seqinfo") stack <- GenomicFiles::VcfStack(files, seqinfo) gr <- as(GenomicFiles::seqinfo(stack)[rownames(stack)], "GRanges") ## RangedVcfStack rgstack <- GenomicFiles::RangedVcfStack(stack, rowRanges = gr) rgstack ## ----constructor3---------------------------------------------------------- vcfFields(rgstack)$geno VCFArray(rgstack, name = "SB") ## ----remote, eval=FALSE---------------------------------------------------- # chr22url <- "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz" # chr22url.tbi <- paste0(chr22url, ".tbi") # va <- VCFArray(chr22url, vindex =chr22url.tbi, name = "GT") ## ---- seedAccessor--------------------------------------------------------- va <- VCFArray(fl, name = "GT") seed(va) ## ---- vcffileAccessor------------------------------------------------------ vcffile(va) ## ---- dims----------------------------------------------------------------- va <- VCFArray(fl, name = "GT") dim(va) class(dimnames(va)) lengths(dimnames(va)) ## ---- subsetting----------------------------------------------------------- va[1:3, 1:3] va[c(TRUE, FALSE), ] ## ---- numeric-------------------------------------------------------------- ds <- VCFArray(fl, name = "DS") log(ds+5) ## ---- VCFArraySeed--------------------------------------------------------- seed <- VCFArray:::VCFArraySeed(fl, name = "GT", pfix = NULL) seed path(vcffile(seed)) ## ---- VCFArray-from-VCFArraySeed------------------------------------------- (va <- VCFArray(seed)) ## ---- da------------------------------------------------------------------- da <- DelayedArray(seed) class(da) all.equal(da, va) ## -------------------------------------------------------------------------- sessionInfo()