## ----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---------------------------------------------------------------- library(GDSArray) file <- GDSArray::gdsExampleFileName("seqgds") gdsnodes(file) GDSArray(file, "genotype/data") GDSArray(file, "sample.id") ## ----makeVariantExperimentFromGDS--------------------------------------------- ve <- makeVariantExperimentFromGDS(file) ve ## ----showAvailable------------------------------------------------------------ args(makeVariantExperimentFromGDS) showAvailable(file) ## ----makeVariantExperimentFromGDS2-------------------------------------------- assays(ve) assay(ve, 1) GDSArray(file, "genotype/data") ## original GDSArray from GDS file before permutation ## ----rrrd--------------------------------------------------------------------- rowRanges(ve) rowData(ve) ## ----colData------------------------------------------------------------------ colData(ve) ## ----gdsfile------------------------------------------------------------------ gdsfile(ve) ## ----metaData----------------------------------------------------------------- metadata(ve) ## ----makeVariantExperimentFromVCF--------------------------------------------- vcf <- SeqArray::seqExampleFileName("vcf") ve <- makeVariantExperimentFromVCF(vcf, out.dir = tempfile()) ve ## ----retrieve GDS------------------------------------------------------------- gdsfile(ve) ## ----makeVariantExperimentFromVCF2-------------------------------------------- assay(ve, 1) ## ----makeVariantExperimentFromVCF3-------------------------------------------- rowData(ve) ## ----sampleInfo--------------------------------------------------------------- sampleInfo <- system.file("extdata", "Example_sampleInfo.txt", package="VariantExperiment") vevcf <- makeVariantExperimentFromVCF(vcf, sample.info = sampleInfo) colData(vevcf) ## ----makeVariantExperimentFromVCFArgs----------------------------------------- vevcf1 <- makeVariantExperimentFromVCF(vcf, info.import=c("OR", "GP")) rowData(vevcf1) ## ----makeVariantExperimentFromVCFArgs_startCount------------------------------ vevcf2 <- makeVariantExperimentFromVCF(vcf, start=101, count=1000) vevcf2 ## ----makeVariantExperimentFromGDS_seq----------------------------------------- gds <- SeqArray::seqExampleFileName("gds") ve <- makeVariantExperimentFromGDS(gds) ve ## ----showAvailable1----------------------------------------------------------- showAvailable(gds) ## ----makeVariantExperimentFromGDSArgs----------------------------------------- ve3 <- makeVariantExperimentFromGDS(gds, rowDataColumns = c("allele", "annotation/id"), infoColumns = c("AC", "AN", "DP"), rowDataOnDisk = TRUE, colDataOnDisk = FALSE) rowData(ve3) ## DelayedDataFrame object colData(ve3) ## DataFrame object ## ----------------------------------------------------------------------------- veseq <- makeVariantExperimentFromGDS(file, rowDataColumns = c("allele"), infoColumns = character(0)) rowData(veseq) ## ----makeVariantExperimentFromGDS_snp----------------------------------------- snpfile <- SNPRelate::snpgdsExampleFileName() vesnp <- makeVariantExperimentFromGDS(snpfile, rowDataColumns = c("snp.allele")) rowData(vesnp) ## ---- 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 ## ----saveVE------------------------------------------------------------------- a <- tempfile() ve2 <- saveVariantExperiment(ve1, dir=a, replace=TRUE, chunk_size = 30) ## ----loadVE------------------------------------------------------------------- ve3 <- loadVariantExperiment(dir=a) gdsfile(ve3) all.equal(ve2, ve3) ## ----sessionInfo-------------------------------------------------------------- sessionInfo()