Nothing
## ----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()
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.