## ---- message=FALSE------------------------------------------------------ library(hiReadsProcessor) ## added to avoid package build failure on windows machines ## if(.Platform$OS.type == "windows") { register(SerialParam()) } ## ------------------------------------------------------------------------ runData <- system.file("extdata/FLX_sample_run/", package = "hiReadsProcessor") list.files(runData, recursive = TRUE) ## ------------------------------------------------------------------------ seqProps <- read.SeqFolder(runData, seqfilePattern = ".+fna.gz$") seqProps ## ------------------------------------------------------------------------ seqProps$sectors$"1"$samples ## ------------------------------------------------------------------------ seqProps <- findBarcodes(seqProps, sector = "all", showStats = TRUE) seqProps seqProps$sectors ## ------------------------------------------------------------------------ load(file.path(system.file("data", package = "hiReadsProcessor"), "FLX_seqProps.RData")) ## ---- eval=FALSE--------------------------------------------------------- # seqProps <- findPrimers(seqProps, showStats=TRUE) ## ---- eval=FALSE--------------------------------------------------------- # seqProps <- findLTRs(seqProps, showStats=TRUE) ## ---- eval=FALSE--------------------------------------------------------- # seqProps <- findVector(seqProps, showStats = TRUE) ## ---- eval=FALSE--------------------------------------------------------- # seqProps <- findLinkers(seqProps, showStats=TRUE, doRC=TRUE) ## ---- eval=FALSE--------------------------------------------------------- # seqProps <- findIntegrations(seqProps, # genomeIndices = c("hg18" = "/usr/local/genomeIndexes/hg18.noRandom.2bit"), # numServers = 2) ## ------------------------------------------------------------------------ sampleSummary(seqProps) ## ------------------------------------------------------------------------ sessionInfo()