R: Create a 'EpiTxDb' object from a 'GRanges' object

makeEpiTxDbFromGRanges {EpiTxDb}

R Documentation

Create a `EpiTxDb` object from a `GRanges` object

Description

makeEpiTxDbFromGRanges extracts informations from a GRanges object. The following metadata columns can be used:

mod_id, mod_type, mod_name and tx_ensembl. The first three are mandatory, whereas tx_ensembl is optional.
rx_genename, rx_rank, rx_ensembl, rx_ensembltrans and rx_entrezid
spec_type, spec_genename, spec_ensembl, spec_ensembltrans and spec_entrezid
ref_type and ref

... and passed on the makeEpiTxDb.

Usage

makeEpiTxDbFromGRanges(gr, metadata = NULL, reassign.ids = FALSE)

Arguments

`gr`	A `GRanges` object, which contains at least the mandatory columns.
`metadata`	A 2-column `data.frame` containing meta information to be included in the `EpiTxDb` object. This `data.frame` is just passed to `makeEpiTxDb`. See `makeEpiTxDb` for more information about the format of metadata. (default: `metadata = NULL`)
`reassign.ids`	= FALSE

Value

a EpiTxDb object.

Examples

library(GenomicRanges)
gr <- GRanges(seqnames = "test",
              ranges = IRanges::IRanges(1,1),
              strand = "+",
              DataFrame(mod_id = 1L,
                        mod_type = "Am",
                        mod_name = "Am_1"))
etdb <- makeEpiTxDbFromGRanges(gr)