## ---- 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()
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