## ----options, eval=TRUE, echo=FALSE---------------------------------------- options(showHeadLines=3) options(showTailLines=3) ## ----getPackage, eval=FALSE------------------------------------------------ # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("VariantExperiment") ## ---- eval = FALSE--------------------------------------------------------- # BiocManager::install(“Bioconductor/VariantExperiment”) ## ----Load, message=FALSE--------------------------------------------------- library(VariantExperiment) ## ---- GDSArray------------------------------------------------------------- gds <- SeqArray::seqExampleFileName("gds") GDSArray(gds, "genotype/data") GDSArray(gds, "sample.id") ## ----makeVariantExperimentFromGDS------------------------------------------ ve <- makeVariantExperimentFromGDS(gds) ve ## ----makeVariantExperimentFromGDS2----------------------------------------- assays(ve) assay(ve, 1) ## ----rrrd------------------------------------------------------------------ rowRanges(ve) rowData(ve) ## ----colData--------------------------------------------------------------- colData(ve) ## ----gdsfile--------------------------------------------------------------- gdsfile(ve) ## ----metaData-------------------------------------------------------------- metadata(ve) ## ---- 2d------------------------------------------------------------------- ve[1:10, 1:5] ## ----colDataExtraction----------------------------------------------------- colData(ve) ve[, as.logical(ve$family == "1328")] ## ----rowDataExtraction----------------------------------------------------- rowData(ve) ve[as.logical(rowData(ve)$REF == "T"),] ## ----overlap--------------------------------------------------------------- ve1 <- subsetByOverlaps(ve, GRanges("22:1-48958933")) ve1 ## ----saveLoad, eval=FALSE-------------------------------------------------- # hwe(ve1) # ## Error in .saveGDSMaybe(gdsfile) : use # ## 'saveVariantExperiment()' to synchronize on-disk and # ## in-memory representations ## ----saveVE---------------------------------------------------------------- a <- tempfile() ve2 <- saveVariantExperiment(ve1, dir=a, replace=TRUE) ## ----loadVE---------------------------------------------------------------- ve3 <- loadVariantExperiment(dir=a) gdsfile(ve3) all.equal(ve2, ve3) ## ----newVEstats------------------------------------------------------------ head(hwe(ve2)) ## ----sessionInfo----------------------------------------------------------- sessionInfo()