## ----style, echo = FALSE, results = 'asis'------------------------------------ BiocStyle::markdown(css.files = c('custom.css')) ## ---- echo = FALSE------------------------------------------------------------ suppressPackageStartupMessages({ library(rtracklayer) library(Rsamtools) library(GenomicFeatures) library(RNAmodR.Data) library(RNAmodR) }) ## ---- eval = FALSE------------------------------------------------------------ # library(rtracklayer) # library(Rsamtools) # library(GenomicFeatures) # library(RNAmodR.Data) # library(RNAmodR) ## ----example_files, message=FALSE, results='hide'----------------------------- annotation <- GFF3File(RNAmodR.Data.example.gff3()) sequences <- RNAmodR.Data.example.fasta() files <- c(Treated = RNAmodR.Data.example.bam.1(), Treated = RNAmodR.Data.example.bam.2(), Treated = RNAmodR.Data.example.bam.3()) ## ----seqdata------------------------------------------------------------------ seqdata <- End5SequenceData(files, annotation = annotation, sequences = sequences) seqdata ## ----seqdata_functions, message=FALSE, results='hide'------------------------- names(seqdata) # matches the transcript names as returned by a TxDb object colnames(seqdata) # returns a CharacterList of all column names bamfiles(seqdata) ranges(seqdata) # generate from a TxDb object sequences(seqdata) seqinfo(seqdata) ## ----seqdata2----------------------------------------------------------------- seqdata[1] sdf <- seqdata[[1]] sdf ## ----seqdata2_functions, message=FALSE, results='hide'------------------------ names(sdf) # this returns the columns names of the data ranges(sdf) sequences(sdf) ## ----seqdata2_subset---------------------------------------------------------- sdf[,1:2] sdf[1:3,] ## ----modifier1---------------------------------------------------------------- mi <- ModInosine(files, annotation = annotation, sequences = sequences) ## ----modifier1_functions, message=FALSE, results='hide'----------------------- names(mi) # matches the transcript names as returned by a TxDb object bamfiles(mi) ranges(mi) # generated from a TxDb object sequences(mi) seqinfo(mi) sequenceData(mi) # returns the SequenceData ## ----settings----------------------------------------------------------------- settings(mi) settings(mi,"minScore") settings(mi) <- list(minScore = 0.5) settings(mi,"minScore") ## ----message=TRUE, message=FALSE, results='hide'------------------------------ sequences <- RNAmodR.Data.example.AAS.fasta() annotation <- GFF3File(RNAmodR.Data.example.AAS.gff3()) files <- list("SampleSet1" = c(treated = RNAmodR.Data.example.wt.1(), treated = RNAmodR.Data.example.wt.2(), treated = RNAmodR.Data.example.wt.3()), "SampleSet2" = c(treated = RNAmodR.Data.example.bud23.1(), treated = RNAmodR.Data.example.bud23.2()), "SampleSet3" = c(treated = RNAmodR.Data.example.trm8.1(), treated = RNAmodR.Data.example.trm8.2())) ## ----modifierset1------------------------------------------------------------- msi <- ModSetInosine(files, annotation = annotation, sequences = sequences) ## ----modifierset2------------------------------------------------------------- names(msi) msi[[1]] ## ----modifierset1_functions, message=FALSE, results='hide'-------------------- bamfiles(msi) ranges(msi) # generate from a TxDb object sequences(msi) seqinfo(msi) ## ----results1----------------------------------------------------------------- mod <- modifications(msi) mod[[1]] ## ----results2----------------------------------------------------------------- mod <- modifications(msi, perTranscript = TRUE) mod[[1]] ## ----coord-------------------------------------------------------------------- mod <- modifications(msi) coord <- unique(unlist(mod)) coord$score <- NULL coord$sd <- NULL compareByCoord(msi,coord) ## ----------------------------------------------------------------------------- txdb <- makeTxDbFromGFF(annotation) alias <- data.frame(tx_id = names(id2name(txdb)), name = id2name(txdb)) ## ----plot1, fig.cap="Heatmap for identified Inosine positions.", fig.asp=1---- plotCompareByCoord(msi, coord, alias = alias) ## ----plot2, fig.cap="Heatmap for identified Inosine positions with normalized scores.", fig.asp=1---- plotCompareByCoord(msi[c(3,1,2)], coord, alias = alias, normalize = "SampleSet3", perTranscript = TRUE) ## ----plot3, fig.cap="Scores along a transcript containing a A to G conversion indicating the presence of Inosine.", fig.asp=1---- plotData(msi, "2", from = 10L, to = 45L, alias = alias) # showSequenceData = FALSE ## ----plot4, fig.cap="Scores along a transcript containing a A to G conversion indicating the presence of Inosine. This figure includes the detailed pileup sequence data.", fig.asp=1.2---- plotData(msi[1:2], "2", from = 10L, to = 45L, showSequenceData = TRUE, alias = alias) ## ----plot6, fig.cap="TPR vs. FPR plot.", fig.asp=1---------------------------- plotROC(msi, coord) ## ----------------------------------------------------------------------------- sessionInfo()