## ----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") #> deactivate temporarily 3/4/20 ## ---- GDSMatrix--------------------------------------------------------------- GDSArray(file, "annotation/format/DP") ## ---- GDSFile----------------------------------------------------------------- gf <- GDSFile(file) gf$annotation$info gf$annotation$info$AC ## ---- seedAccessor------------------------------------------------------------ #> ga <- GDSArray(file, "genotype") #> deactivate temporarily 3/4/20 #> seed(ga) ## ---- gdsfileAccessor--------------------------------------------------------- #> gdsfile(ga) ## ---- gdsnodes---------------------------------------------------------------- gdsnodes(file) identical(gdsnodes(file), gdsnodes(gf)) GDSArray(file, name=gdsnodes(file)[2]) ## ---- dims-------------------------------------------------------------------- ga <- GDSArray(file, "annotation/format/DP") 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") dp log(dp) dp[rowMeans(dp) < 60, ] ## ---- GDSArraySeed------------------------------------------------------------ #> seed <- GDSArray:::GDSArraySeed(file, "genotype") #> deactivate temporarily 3/4/20 #> seed ## ---- GDSArray-from-GDSArraySeed---------------------------------------------- #> GDSArray(seed) ## ---- da---------------------------------------------------------------------- #> class(DelayedArray(seed)) ## ---- sessionInfo------------------------------------------------------------- sessionInfo()