In FelixErnst/EpiTxDb.Hs.hg38: Annotation package for EpiTxDb objects

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Available resources

EpiTxDb.Hs.hg38 contains post-transcriptional RNA modifications from RMBase v2.0 [@Xuan.2017], tRNAdb [@Juehling.2009] and snoRNAdb [@Lestrade.2006] and can be accessed through the functions EpiTxDb.Hs.hg38.tRNAdb(), EpiTxDb.Hs.hg38.snoRNAdb() and EpiTxDb.Hs.hg38.RMBase()

suppressPackageStartupMessages({
  library(EpiTxDb.Hs.hg38)
})

library(EpiTxDb.Hs.hg38)

etdb <- EpiTxDb.Hs.hg38.tRNAdb()
etdb

Modification information can be accessed through the typical function for an EpiTxDb object, for example modifications():

modifications(etdb)

For a more detailed overview and explanation of the functionality of the EpiTxDb class, have a look at the EpiTxDb package.

Chain files for rRNA

The rRNA sequence annotation for ribosomal RNA has undergone some clarification processes in recent years. Therefore some of the annotation of modification refer to an older rRNA annotation.

In order to help using and updating older information, a chain file was generated for use with liftOver, which allows conversion of hg19 coordinates to hg38 coordinates and back. The resources can be loaded via chain.rRNA.hg19Tohg38() and chain.rRNA.hg38Tohg19().

cf <- chain.rRNA.hg19Tohg38()
cf

The following example illustrate a use case, in which data from the Modomics [@Boccaletto.2018] database will be used. The sequence data currently stored, is the hg19 version. First we load the sequence as ModRNAStringSet.

library(rtracklayer)
library(Modstrings)
files <- c(system.file("extdata","Modomics.LSU.Hs.txt",
                       package = "EpiTxDb.Hs.hg38"),
           system.file("extdata","Modomics.SSU.Hs.txt",
                       package = "EpiTxDb.Hs.hg38"))
seq <- lapply(files,readLines,encoding = "UTF-8")
seq <- unlist(seq)
names <- seq[seq.int(1L,6L,2L)]
seq <- seq[seq.int(2L,6L,2L)]
seq <- ModRNAStringSet(sanitizeFromModomics(gsub("-","",seq)))
names(seq) <- c("28S","5.8S","18S")
mod <- separate(seq)

The position for the one m7G and two m6A are of for the current rRNA sequences. This is also the case for the other modifications.

mod[mod$mod == "m7G" | mod$mod == "m6A"]

Using the chain file we can liftOver the coordinates, which matches the expected coordinates.

mod_new <- unlist(liftOver(mod,cf))
mod_new[mod_new$mod == "m7G" | mod_new$mod == "m6A"]

In addition, the ModRNAStringSet object can be update with the current sequence.

rna <- getSeq(snoRNA.targets.hg38())
names(rna)[1:4] <- c("5S","18S","5.8S","28S")
seqtype(rna) <- "RNA"
seq_new <- combineIntoModstrings(rna, mod_new)
seq_new