## ----style, echo = FALSE, results = 'asis'------------------------------------ BiocStyle::markdown(css.files = c('custom.css')) ## ---- echo=FALSE-------------------------------------------------------------- suppressPackageStartupMessages({ library(RNAmodR.Data) }) ## ---- eval=FALSE-------------------------------------------------------------- # library(RNAmodR.Data) ## ----------------------------------------------------------------------------- eh <- ExperimentHub() ExperimentHub::listResources(eh, "RNAmodR.Data") ## ---- echo=FALSE-------------------------------------------------------------- suppressPackageStartupMessages({ library(GenomicRanges) }) ## ---- eval=FALSE-------------------------------------------------------------- # library(GenomicRanges) ## ----------------------------------------------------------------------------- table <- read.csv2(RNAmodR.Data.snoRNAdb(), stringsAsFactors = FALSE) head(table, n = 2) # keep only the current coordinates table <- table[,1:7] snoRNAdb <- GRanges(seqnames = table$hgnc_symbol, ranges = IRanges(start = table$position, width = 1),strand = "+", type = "RNAMOD", mod = table$modification, Parent = table$hgnc_symbol, Activity = CharacterList(strsplit(table$guide,","))) # convert to current gene name snoRNAdb <- snoRNAdb[vapply(snoRNAdb$Activity != "unknown",all,logical(1)),] snoRNAdb <- split(snoRNAdb,snoRNAdb$Parent) head(snoRNAdb) ## ----------------------------------------------------------------------------- sessionInfo()