makeEpiTxDb {EpiTxDb} | R Documentation

## Creating a `EpiTxDb` from user supplied annotations as `data.frame`s

### Description

`makeEpiTxDb` is a low-level constructor for creating a `EpiTxDb` object from user supplied annotations.

This functions typically will not be used by regular users.

### Usage

    makeEpiTxDb(
      modifications,
      reactions = NULL,
      specifiers = NULL,
      references = NULL,
      metadata = NULL,
      reassign.ids = FALSE
    )

### Arguments

`modifications` | A `data.frame` containg the following columns: `mod_id`: a unique `integer` value per modification. `mod_type`: the modification type as a `character` or `factor` value. Must be a value from `shortName(ModRNAString())`. `mod_name`: a `character` or `factor` name for the specific modification `mod_start`: the start position for the modification as `integer` value. Usually `mod_start = mod_end` `mod_end`: the end position for the modification as `integer` value. Usually `mod_start = mod_end` `mod_strand`: the strand information for the modificaion as a `character` or `factor`. `sn_id`: a `integer` value per unique sequence `sn_name`: a `character` or `factor` as sequence name, e.g a chromosome or a transcript identifier like `chr1`. The first six are mandatory, whereas one of the last two has to be set. `sn_id` will be generated from `sn_name`, if `sn_id` is not set.
`reactions` | An optional `data.frame` containg the following columns: `mod_id`: a `integer` value per modification and the link to the `modification` `data.frame`. `rx_genename`: a `character` or `factor` referencing a genename for the enzyme incorporating the modification. `rx_rank`: a `integer` for sorting enzyme reactions, if multiple enzymes are involved in the modification's incorporation/maintenance. `rx_ensembl`: a `character` or `factor` with an ensembl identifier for the genename of the enzyme. `rx_ensembltrans`: a `character` or `factor` with an ensembl identifier for the transcript being translated into the enzyme. `rx_entrezid`: a `character` or `factor` with an entrezid for the genename of the enzyme. (default: `reactions = NULL`)
`specifiers` | An optional `data.frame` containg the following columns: `mod_id`: a `integer` value per modification and the link to the `modification` `data.frame`. `spec_type`: a `character` or `factor` referencing a type of specifier, e.g. `snoRNA`. Not checked for validity. `spec_genename`: a `character` or `factor` referencing a genename for the specifier directing an enzyme to the specific location for the modification to be incorporated. `spec_ensembl`: a `character` or `factor` with an ensembl identifier for the genename of the specifier. `spec_ensembltrans`: a `character` or `factor` with an ensembl identifier for the transcript being translated into the specifier. `spec_entrezid`: a `character` or `factor` with an entrezid for the genename of the specifier. (default: `specifiers = NULL`)
`references` | An optional `data.frame` containg the following columns: `mod_id`: a `integer` value per modification and the link to the `modification` `data.frame`. `ref_type`: a `character` or `factor` with a reference type, e.g. `PMID`. Is not checked for validity. `ref`: a `character` or `factor` with a reference value, e.g. a specific pubmed id or an journal article. Is not checked for validity. (default: `references = NULL`)
`metadata` | An optional `data.frame` containg the following columns: `name`: a `character` value used as name `value`: a `character` value This dataframe will be returned by `metadata()` (default: `metadata = NULL`)
`reassign.ids` | `TRUE` or `FALSE` Controls how internal `mod_id`s should be assigned. If `reassign.ids` is `FALSE` (the default) and if the ids are supplied, then they are used as the internal ids, otherwise the internal ids are assigned in a way that is compatible with the order defined by ordering the modifications first by chromosome, then by strand, then by start, and finally by end.

### Value

a `EpiTxDb` object.

### See Also

- `makeEpiTxDbFromGRanges` for creating a `EpiTxDb` object from a `GRanges` object and it's metadata columns

- `makeEpiTxDbFromRMBase` for creating a `EpiTxDb` object from RMBase online resources

- `makeEpiTxDbFromtRNAdb` for creating a `EpiTxDb` object from tRNAdb online resources

- `shortName` and `ModRNAString` for information on `ModRNAString` objects.

### Examples

    mod <- data.frame("mod_id" = 1L,
                      "mod_type" = "m1A",
                      "mod_name" = "m1A_1",
                      "mod_start" = 1L,
                      "mod_end" = 1L,
                      "mod_strand" = "+",
                      "sn_id" = 1L,
                      "sn_name" = "test")
    rx <- data.frame(mod_id = 1L,
                     rx_genename = "test",
                     rx_rank = 1L,
                     rx_ensembl = "test",
                     rx_ensembltrans = "test",
                     rx_entrezid = "test")
    spec <- data.frame(mod_id = 1L,
                       spec_type = "test",
                       spec_genename = "test",
                       spec_ensembl = "test",
                       spec_ensembltrans = "test",
                       spec_entrezid = "test")
    ref <- data.frame(mod_id = 1L,
                      ref_type = "test",
                      ref = "test")
    etdb <- makeEpiTxDb(mod,rx,spec,ref)

[Package EpiTxDb version 1.0.0 Index]