## ----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 <- gdsExampleFileName("seqgds") GDSArray(file, "genotype/data") ## ----GDSMatrix---------------------------------------------------------------- GDSArray(file, "annotation/format/DP/data") ## ----GDSFile------------------------------------------------------------------ gf <- GDSFile(file) gf$annotation$info gf$annotation$info$AC ## ----seedAccessor------------------------------------------------------------- gt <- GDSArray(file, "genotype/data") seed(gt) ## ----gdsfileAccessor---------------------------------------------------------- gdsfile(gt) ## ----gdsnodes----------------------------------------------------------------- gdsnodes(file) identical(gdsnodes(file), gdsnodes(gf)) varname <- gdsnodes(file)[2] GDSArray(file, varname) ## ----dims--------------------------------------------------------------------- dp <- GDSArray(file, "annotation/format/DP/data") dim(dp) class(dimnames(dp)) lengths(dimnames(dp)) ## ----methods------------------------------------------------------------------ dp[1:3, 10:15] dp[c(TRUE, FALSE), ] ## ----numeric------------------------------------------------------------------ log(dp) dp[rowMeans(dp) < 60, ] ## ----GDSArraySeed------------------------------------------------------------- gds <- openfn.gds(file) seed <- GDSArray:::GDSArraySeed(gds, "genotype/data") seed closefn.gds(gds) ## ----GDSArray-from-GDSArraySeed----------------------------------------------- GDSArray(seed) ## ----da----------------------------------------------------------------------- class(DelayedArray(seed)) ## ----sessionInfo-------------------------------------------------------------- sessionInfo()