inst/doc/VariantExperiment-class.R

In VariantExperiment: A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend

## ----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----------------------------------------------------------------
file <- SeqArray::seqExampleFileName("gds")
GDSArray(file, "genotype")
GDSArray(file, "sample.id")

## ----makeVariantExperimentFromGDS---------------------------------------------
ve <- makeVariantExperimentFromGDS(file)
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()