## ----style, echo = FALSE, results = 'asis'------------------------------------ BiocStyle::markdown(css.files = c('custom.css')) ## ----echo = FALSE------------------------------------------------------------- suppressPackageStartupMessages({ library(rtracklayer) library(GenomicRanges) library(RNAmodR.RiboMethSeq) library(RNAmodR.Data) }) ## ----eval = FALSE------------------------------------------------------------- # library(rtracklayer) # library(GenomicRanges) # library(RNAmodR.RiboMethSeq) # library(RNAmodR.Data) ## ----message=FALSE, results='hide'-------------------------------------------- annotation <- GFF3File(RNAmodR.Data.example.RMS.gff3()) sequences <- RNAmodR.Data.example.RMS.fasta() files <- list("Sample1" = c(treated = RNAmodR.Data.example.RMS.1()), "Sample2" = c(treated = RNAmodR.Data.example.RMS.2())) ## ----------------------------------------------------------------------------- msrms <- ModSetRiboMethSeq(files, annotation = annotation, sequences = sequences) msrms ## ----------------------------------------------------------------------------- table <- read.csv2(RNAmodR.Data.snoRNAdb(), stringsAsFactors = FALSE) table <- table[table$hgnc_id == "53533",] # Subset to RNA5.8S # keep only the current coordinates table <- table[,1L:7L] snoRNAdb <- GRanges(seqnames = "chr1", ranges = IRanges(start = table$position, width = 1), strand = "+", type = "RNAMOD", mod = table$modification, Parent = "1", #this is the transcript id Activity = IRanges::CharacterList(strsplit(table$guide,","))) coord <- split(snoRNAdb,snoRNAdb$Parent) ## ----------------------------------------------------------------------------- ranges(msrms) alias <- data.frame(tx_id = "1", name = "5.8S rRNA", stringsAsFactors = FALSE) ## ----plot1, fig.cap="Heatmap showing RiboMethSeq scores for 2'-O methylated positions on the 5.8S rRNA."---- plotCompareByCoord(msrms[c(2L,1L)], coord, alias = alias) ## ----plot2, fig.cap="RiboMethSeq scores around Um(14) on 5.8S rRNA.", fig.asp=1---- singleCoord <- coord[[1L]][1L,] plotDataByCoord(msrms, singleCoord) ## ----plot3, fig.cap="RiboMethSeq scores around Um(14) on 5.8S rRNA. Sequence data is shown by setting `showSequenceData = TRUE`.", fig.asp=1---- singleCoord <- coord[[1L]][1L,] plotDataByCoord(msrms, singleCoord, showSequenceData = TRUE) ## ----plot4, fig.cap="TPR versus FPR plot.", fig.asp=1------------------------- plotROC(msrms,coord) ## ----settings----------------------------------------------------------------- settings(msrms) <- list(minScoreMean = 0.7) msrms ## ----udpate------------------------------------------------------------------- msrms2 <- modify(msrms,force = TRUE) ## ----sessioninfo-------------------------------------------------------------- sessionInfo()