## -----------------------------------------------------------------------------
library(scanMiRApp)
# anno <- ScanMiRAnno("Rnor_6")
# for this vignette, we'll work with a lightweight fake annotation:
anno <- ScanMiRAnno("fake")
anno

## -----------------------------------------------------------------------------
seq <- getTranscriptSequence("ENSTFAKE0000056456", anno)
seq

## -----------------------------------------------------------------------------
plotSitesOnUTR(tx="ENSTFAKE0000056456", annotation=anno, miRNA="hsa-miR-155-5p")

## -----------------------------------------------------------------------------
m <- runFullScan(anno)
m

## ----eval=FALSE---------------------------------------------------------------
#  scanMiRApp( list( nameOfAnnotation=anno ) )

## ----eval=FALSE---------------------------------------------------------------
#  # not run
#  anno <- ScanMiRAnno("Rnor_6")
#  saveIndexedFst(readRDS("scan.rds"), "seqnames", file.prefix="out_path/scan")
#  saveIndexedFst(readRDS("aggregated.rds"), "miRNA",
#                 file.prefix="out_path/aggregated")
#  anno$scan <- loadIndexedFst("out_path/scan")
#  anno$aggregated <- loadIndexedFst("out_path/aggregated")
#  # then launch the app
#  scanMiRApp(list(Rnor_6=anno))

## ----sessionInfo, echo=FALSE--------------------------------------------------
sessionInfo()