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

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

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)

EpiTxDb documentation built on March 26, 2021, 6 p.m.