## ----include=FALSE------------------------------------------------------------ library(BiocStyle) ## ----echo = FALSE, out.width="35%", fig.align = 'right'----------------------- knitr::include_graphics(system.file('docs', 'sticker.svg', package = 'scanMiR')) ## ----------------------------------------------------------------------------- library(scanMiR) # seed sequence of hsa-miR-155-5p seed <- "AGCAUUAA" # load a sample transcript data("SampleTranscript") # run scan matches <- findSeedMatches(SampleTranscript, seed, verbose = FALSE) matches ## ----------------------------------------------------------------------------- # full sequence of the mature miR-155-5p transcript miRNA <- "UUAAUGCUAAUCGUGAUAGGGGUU" # run scan matches <- findSeedMatches(SampleTranscript, miRNA, verbose = FALSE) matches ## ----------------------------------------------------------------------------- viewTargetAlignment(matches[1], miRNA, SampleTranscript) ## ----------------------------------------------------------------------------- # load sample KdModel data("SampleKdModel") # run scan matches <- findSeedMatches(SampleTranscript, SampleKdModel, verbose = FALSE) matches ## ----echo = FALSE, out.width="80%", fig.align = 'right', fig.cap="Adapted from Grimson et al. 2007"---- knitr::include_graphics(system.file('docs', 'sitetypes.jpg', package = 'scanMiR')) ## ----message = FALSE---------------------------------------------------------- library(Biostrings) # generate set of random sequences seqs <- DNAStringSet(getRandomSeq(length = 1000, n = 10)) # add vector of ORF lengths mcols(seqs)$ORF.length <- sample(500:800, length(seqs)) # run scan matches2 <- findSeedMatches(seqs, SampleKdModel, verbose = FALSE) head(matches2) ## ----------------------------------------------------------------------------- viewTargetAlignment(matches[1], SampleKdModel, SampleTranscript) ## ----------------------------------------------------------------------------- agg_matches <- aggregateMatches(matches2) head(agg_matches) ## ----------------------------------------------------------------------------- unlist(scanMiR:::.defaultAggParams()) ## ----sessionInfo, echo=FALSE-------------------------------------------------- sessionInfo()