## ----options, eval=TRUE, echo=FALSE------------------------------------------- options(showHeadLines=3) options(showTailLines=3) ## ----Load, message=FALSE------------------------------------------------------ library(VariantExperiment) ## ----makeVariantExperimentFromVCF, eval=FALSE--------------------------------- # vcf <- SeqArray::seqExampleFileName("vcf") # ve <- makeVariantExperimentFromVCF(vcf) # ve ## ----retrieve GDS, eval=FALSE------------------------------------------------- # gdsfile(ve) ## ----makeVariantExperimentFromVCF2, eval=FALSE-------------------------------- # assay(ve, 1) ## ----makeVariantExperimentFromVCF3, eval=FALSE-------------------------------- # rowData(ve) ## ----sampleInfo, eval=FALSE--------------------------------------------------- # sampleInfo <- system.file("extdata", "Example_sampleInfo.txt", # package="VariantExperiment") # ve <- makeVariantExperimentFromVCF(vcf, sample.info = sampleInfo) # colData(ve) ## ----makeVariantExperimentFromVCFArgs, eval=FALSE----------------------------- # ve1 <- makeVariantExperimentFromVCF(vcf, info.import=c("OR", "GP")) # rowData(ve1) ## ----makeVariantExperimentFromVCFArgs_startCount, eval=FALSE------------------ # ve2 <- makeVariantExperimentFromVCF(vcf, start=101, count=1000) # ve2 ## ----makeVariantExperimentFromGDS, eval=FALSE--------------------------------- # gds <- SeqArray::seqExampleFileName("gds") # ve <- makeVariantExperimentFromGDS(gds) # ve ## ----makeVariantExperimentFromGDS2, eval=FALSE-------------------------------- # rowData(ve) # colData(ve) ## ----showAvailable, eval=FALSE------------------------------------------------ # showAvailable(gds) ## ----makeVariantExperimentFromGDSArgs, eval=FALSE----------------------------- # ve3 <- makeVariantExperimentFromGDS(gds, # rowDataColumns = c("ID", "ALT", "REF"), # infoColumns = c("AC", "AN", "DP"), # rowDataOnDisk = TRUE, # colDataOnDisk = FALSE) # rowData(ve3) ## DelayedDataFrame object # colData(ve3) ## DataFrame object ## ----stats, eval=FALSE-------------------------------------------------------- # ## sample missing rate # mr.samp <- seqMissing(ve, per.variant = FALSE) # head(mr.samp) # ## hwe # hwe <- hwe(ve) # head(hwe) # ## titv ratio by sample / overall # titv <- titv(ve, by.sample=TRUE) # head(titv) # titv(ve, by.sample=FALSE) # ## countSingletons # countSingletons(ve) ## ----sessionInfo-------------------------------------------------------------- sessionInfo()