inst/doc/EpiTxDb-creation.R

In EpiTxDb: Storing and accessing epitranscriptomic information using the AnnotationDbi interface

## ----style, echo = FALSE, results = 'asis'------------------------------------
BiocStyle::markdown(css.files = c('custom.css'))

## ---- echo = FALSE------------------------------------------------------------
suppressPackageStartupMessages({
    library(GenomicRanges)
    library(EpiTxDb)
})

## ---- eval = FALSE------------------------------------------------------------
#  library(GenomicRanges)
#  library(EpiTxDb)

## -----------------------------------------------------------------------------
gr <- GRanges(seqnames = "test",
              ranges = IRanges::IRanges(1,1),
              strand = "+",
              DataFrame(mod_id = 1L,
                        mod_type = "Am",
                        mod_name = "Am_1"))
etdb <- makeEpiTxDbFromGRanges(gr, metadata = data.frame(name = "test",
                                                         value = "Yes"))
etdb
metadata(etdb)

## -----------------------------------------------------------------------------
etdb <- makeEpiTxDbFromtRNAdb("Saccharomyces cerevisiae")
etdb

## ---- eval=FALSE--------------------------------------------------------------
#  etdb <- makeEpiTxDbFromRMBase(organism = "Saccharomyces cerevisiae",
#                                genome = "sacCer3",
#                                modtype = "m1A")

## -----------------------------------------------------------------------------
sessionInfo()