## ----style, echo = FALSE, results = 'asis'------------------------------------ BiocStyle::markdown(css.files = c('custom.css')) ## ---- echo = FALSE------------------------------------------------------------ suppressPackageStartupMessages({ library(rtracklayer) library(GenomicRanges) library(RNAmodR.AlkAnilineSeq) library(RNAmodR.Data) }) ## ---- eval = FALSE------------------------------------------------------------ # library(rtracklayer) # library(GenomicRanges) # library(RNAmodR.AlkAnilineSeq) # library(RNAmodR.Data) ## ---- message=FALSE, results='hide'------------------------------------------- annotation <- GFF3File(RNAmodR.Data.example.AAS.gff3()) sequences <- RNAmodR.Data.example.AAS.fasta() files <- list("wt" = c(treated = RNAmodR.Data.example.wt.1(), treated = RNAmodR.Data.example.wt.2(), treated = RNAmodR.Data.example.wt.3()), "Bud23del" = c(treated = RNAmodR.Data.example.bud23.1(), treated = RNAmodR.Data.example.bud23.2()), "Trm8del" = c(treated = RNAmodR.Data.example.trm8.1(), treated = RNAmodR.Data.example.trm8.2())) ## ----------------------------------------------------------------------------- msaas <- ModSetAlkAnilineSeq(files, annotation = annotation, sequences = sequences) msaas ## ----------------------------------------------------------------------------- mod <- modifications(msaas) lapply(mod,head, n = 2L) ## ----------------------------------------------------------------------------- coord <- mod[[1L]] alias <- data.frame(tx_id = c(1L,3L,5L,6L,7L,8L,10L,11L), name = c("18S rRNA","tF(GAA)B","tG(GCC)B","tT(AGT)B", "tQ(TTG)B","tC(GCA)B","tS(CGA)C","tV(AAC)E1"), stringsAsFactors = FALSE) ## ----plot1, fig.cap="Heatmap showing Stop ratio scores for detected m7G, m3C and D positions.", fig.asp=1---- plotCompareByCoord(msaas, coord, score = "scoreSR", alias = alias, normalize = TRUE) ## ----plot2, fig.cap="Heatmap showing Stop ratio scores for detected m7G1575 on the 18S rRNA.", fig.asp=0.5---- plotCompareByCoord(msaas, coord[1L], score = "scoreSR", alias = alias) ## ----plot3, fig.cap="Stop ratio scores for detected m7G1575 on the 18S rRNA plotted as bar plots along the sequence.", fig.asp=1---- plotData(msaas, "1", from = 1550L, to = 1600L) ## ----plot4, fig.cap="Stop ratio scores for detected m7G1575 on the 18S rRNA plotted as bar plots along the sequence. The raw sequence data is shown by setting `showSequenceData = TRUE.", fig.asp=1---- plotData(msaas[1L:2L], "1", from = 1550L, to = 1600L, showSequenceData = TRUE) ## ---- sessioninfo------------------------------------------------------------- sessionInfo()