## ----------------------------------------------------------------------------- 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()