ProteinFunctionality: Protein related functionality

In ensembldb: Utilities to create and use Ensembl-based annotation databases

Description

This help page provides information about most of the functionality related to protein annotations in ensembldb.

The proteins method retrieves protein related annotations from an EnsDb database.

The listUniprotDbs method lists all Uniprot database names in the EnsDb.

The listUniprotMappingTypes method lists all methods that were used for the mapping of Uniprot IDs to Ensembl protein IDs.

The listProteinColumns function allows to conveniently extract all database columns containing protein annotations from an EnsDb database.

Usage

## S4 method for signature 'EnsDb'
proteins(
  object,
  columns = listColumns(object, "protein"),
  filter = AnnotationFilterList(),
  order.by = "",
  order.type = "asc",
  return.type = "DataFrame"
)

## S4 method for signature 'EnsDb'
listUniprotDbs(object)

## S4 method for signature 'EnsDb'
listUniprotMappingTypes(object)

listProteinColumns(object)

Arguments

object	The EnsDb object.
columns	For proteins: character vector defining the columns to be extracted from the database. Can be any column(s) listed by the listColumns method.
filter	For proteins: A filter object extending AnnotationFilter or a list of such objects to select specific entries from the database. See Filter-classes for a documentation of available filters and use supportedFilters to get the full list of supported filters.
order.by	For proteins: a character vector specifying the column(s) by which the result should be ordered.
order.type	For proteins: if the results should be ordered ascending (order.type = "asc") or descending (order.type = "desc")
return.type	For proteins: character of lenght one specifying the type of the returned object. Can be either "DataFrame", "data.frame" or "AAStringSet".

Details

The proteins method performs the query starting from the protein tables and can hence return all annotations from the database that are related to proteins and transcripts encoding these proteins from the database. Since proteins does thus only query annotations for protein coding transcripts, the genes or transcripts methods have to be used to retrieve annotations for non-coding transcripts.

Value

The proteins method returns protein related annotations from an EnsDb object with its return.type argument allowing to define the type of the returned object. Note that if return.type = "AAStringSet" additional annotation columns are stored in a DataFrame that can be accessed with the mcols method on the returned object.

The listProteinColumns function returns a character vector with the column names containing protein annotations or throws an error if no such annotations are available.

Author(s)

Johannes Rainer

Examples

library(ensembldb)
library(EnsDb.Hsapiens.v86)
edb <- EnsDb.Hsapiens.v86
## Get all proteins from tha database for the gene ZBTB16, if protein
## annotations are available
if (hasProteinData(edb))
    proteins(edb, filter = GeneNameFilter("ZBTB16"))

## List the names of all Uniprot databases from which Uniprot IDs are
## available in the EnsDb
if (hasProteinData(edb))
    listUniprotDbs(edb)


## List the type of all methods that were used to map Uniprot IDs to Ensembl
## protein IDs
if (hasProteinData(edb))
    listUniprotMappingTypes(edb)


## List all columns containing protein annotations
library(EnsDb.Hsapiens.v86)
edb <- EnsDb.Hsapiens.v86
if (hasProteinData(edb))
    listProteinColumns(edb)

ensembldb documentation built on Nov. 8, 2020, 4:57 p.m.