In FelixErnst/RNAmodR.Data: Example data for the RNAmodR package

BiocStyle::markdown(css.files = c('custom.css'))

Available resources

RNAmodR.Data contains example data for the RNAmodR and related packages. The data is provided as gff3, fasta and bam files.

Four sets of data with multiple files are included

suppressPackageStartupMessages({
  library(RNAmodR.Data)
})

library(RNAmodR.Data)

eh <- ExperimentHub()
ExperimentHub::listResources(eh, "RNAmodR.Data")

These resources are grouped based on topic. Please have a look at the following man pages:

?RNAmodR.Data.example for general example data used for different purposes
?RNAmodR.Data.RMS for example data for RiboMethSeq
?RNAmodR.Data.AAS for example data for AlkAnilineSeq
?RNAmodR.Data.man for small data set for man page examples
?RNAmodR.Data.snoRNAdb for snoRNAdb as csv file

snoRNAdb

RNAmodR.Data.snoRNAdb consists of a table containing the published data from the snoRNAdb [@Lestrade.2006]. The can be loaded as a GRanges object.

suppressPackageStartupMessages({
  library(GenomicRanges)
})

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)