Creating a EpiTxDb from user supplied annotations as data.frames

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.

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_ids 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.

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)
#> Creating EpiTxDb object ... 
#> done

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

Arguments

Value

See also

Examples