## ----options, eval=TRUE, echo=FALSE---------------------------------------- options(showHeadLines=3) options(showTailLines=3) ## ----getPackage, eval=FALSE------------------------------------------------ # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("GDSArray") ## ----Load, message=FALSE--------------------------------------------------- library(GDSArray) ## ---- GDSArray------------------------------------------------------------- file <- SeqArray::seqExampleFileName("gds") GDSArray(file, "genotype/data") ## ---- GDSMatrix------------------------------------------------------------ GDSArray(file, "phase/data") ## ---- GDSFile-------------------------------------------------------------- gf <- GDSFile(file) gf$annotation$info gf$annotation$info$AC ## ---- seedAccessor--------------------------------------------------------- ga <- GDSArray(file, "genotype/data") seed(ga) ## ---- gdsfileAccessor------------------------------------------------------ gdsfile(ga) ## ---- gdsnodes------------------------------------------------------------- gdsnodes(file) identical(gdsnodes(file), gdsnodes(gf)) GDSArray(file, name=gdsnodes(file)[2]) ## ---- dims----------------------------------------------------------------- ga <- GDSArray(file, "phase/data") dim(ga) class(dimnames(ga)) lengths(dimnames(ga)) ## ---- methods-------------------------------------------------------------- ga[1:3, 10:15] ga[c(TRUE, FALSE), ] ## ---- numeric-------------------------------------------------------------- dp <- GDSArray(file, "annotation/format/DP/data") dp log(dp) dp[rowMeans(dp) < 60, ] ## ---- GDSArraySeed--------------------------------------------------------- seed <- GDSArray:::GDSArraySeed(file, "genotype/data") seed ## ---- GDSArray-from-GDSArraySeed------------------------------------------- GDSArray(seed) ## ---- da------------------------------------------------------------------- class(DelayedArray(seed)) ## ---- sessionInfo---------------------------------------------------------- sessionInfo()