## ----style, echo = FALSE, results = 'asis'------------------------------------ BiocStyle::markdown(css.files = c('custom.css')) ## ----package, echo=FALSE------------------------------------------------------ suppressPackageStartupMessages({ library(Structstrings) }) ## ----package2, eval=FALSE----------------------------------------------------- # if(!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("Structstrings") # library(Structstrings) ## ----annotation_convert------------------------------------------------------- dbs[[2L]] <- convertAnnotation(dbs[[2L]],from = 2L, to = 1L) dbs[[3L]] <- convertAnnotation(dbs[[3L]],from = 3L, to = 1L) dbs[[4L]] <- convertAnnotation(dbs[[4L]],from = 4L, to = 1L) # Note: convertAnnotation checks for presence of annotation and stops # if there is any conflict. dbs ## ----base_pairing------------------------------------------------------------- # base pairing table dbdfl <- getBasePairing(dbs) dbdfl[[1L]] ## ----loopindices-------------------------------------------------------------- loopids <- getLoopIndices(dbs, bracket.type = 1L) loopids[[1L]] # can also be constructed from DotBracketDataFrame and contains the same # information loopids2 <- getLoopIndices(dbdfl, bracket.type = 1L) all(loopids == loopids2) ## ----dotbracket--------------------------------------------------------------- rec_dbs <- getDotBracket(dbdfl) dbdf <- unlist(dbdfl) dbdf$character <- NULL dbdfl2 <- relist(dbdf,dbdfl) # even if the character column is not set, the dot bracket string can be created rec_dbs2 <- getDotBracket(dbdfl2) rec_dbs3 <- getDotBracket(dbdfl, force = TRUE) rec_dbs[[1L]] rec_dbs2[[1L]] rec_dbs3[[1L]] ## ----pseudoloop--------------------------------------------------------------- db <- DotBracketString("((((....[[[))))....((((....<<<<...))))]]]....>>>>...") db getDotBracket(getBasePairing(db), force = TRUE) ## ----structured_rna_string---------------------------------------------------- data("dbs", package = "Structstrings") data("nseq", package = "Structstrings") sdbs <- StructuredRNAStringSet(nseq,dbs) sdbs[1L] # subsetting to element returns the sequence sdbs[[1L]] # dotbracket() gives access to the DotBracketStringSet dotbracket(sdbs)[[1L]] ## ----structured_rna_string_base_pairing--------------------------------------- dbdfl <- getBasePairing(sdbs) dbdfl[[1L]] # returns the result without sequence information dbdfl <- getBasePairing(sdbs, return.sequence = TRUE) dbdfl[[1L]] ## ----------------------------------------------------------------------------- sessionInfo()