## ----style, echo = FALSE, results = 'asis'------------------------------------ BiocStyle::markdown(css.files = c('custom.css')) ## ---- echo=FALSE-------------------------------------------------------------- suppressPackageStartupMessages({ library(EpiTxDb.Hs.hg38) }) ## ---- eval=FALSE-------------------------------------------------------------- # library(EpiTxDb.Hs.hg38) ## ----------------------------------------------------------------------------- etdb <- EpiTxDb.Hs.hg38.tRNAdb() etdb ## ----------------------------------------------------------------------------- modifications(etdb) ## ----------------------------------------------------------------------------- cf <- chain.rRNA.hg19Tohg38() cf ## ----------------------------------------------------------------------------- library(rtracklayer) library(Modstrings) files <- c(system.file("extdata","Modomics.LSU.Hs.txt", package = "EpiTxDb.Hs.hg38"), system.file("extdata","Modomics.SSU.Hs.txt", package = "EpiTxDb.Hs.hg38")) seq <- lapply(files,readLines,encoding = "UTF-8") seq <- unlist(seq) names <- seq[seq.int(1L,6L,2L)] seq <- seq[seq.int(2L,6L,2L)] seq <- ModRNAStringSet(sanitizeFromModomics(gsub("-","",seq))) names(seq) <- c("28S","5.8S","18S") mod <- separate(seq) ## ----------------------------------------------------------------------------- mod[mod$mod == "m7G" | mod$mod == "m6A"] ## ----------------------------------------------------------------------------- mod_new <- unlist(liftOver(mod,cf)) mod_new[mod_new$mod == "m7G" | mod_new$mod == "m6A"] ## ----------------------------------------------------------------------------- rna <- getSeq(snoRNA.targets.hg38()) names(rna)[1:4] <- c("5S","18S","5.8S","28S") seqtype(rna) <- "RNA" seq_new <- combineIntoModstrings(rna, mod_new) seq_new ## ----------------------------------------------------------------------------- sessionInfo()