makeEpiTxDb: Creating a 'EpiTxDb' from user supplied annotations as...

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

Creating a EpiTxDb from user supplied annotations as data.frames

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_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.

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)

FelixErnst/EpiTxDb documentation built on March 31, 2024, 1:21 a.m.