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)

[Package EpiTxDb version 1.2.1 Index]