MirtarbaseDb-AnnotationDbi: Integration into the AnnotationDbi framework

In jotsetung/mirtarbase: mirtarbase: a database of validated miRNA target gene interactions

Description

Several of the methods available for AnnotationDbi objects are also implemented for MirtarbaseDb objects. This enables to extract data from MirtarbaseDb objects in a similar fashion than from objects inheriting from the base annotation package class AnnotationDbi. In addition to the standard usage, the select for MirtarbaseDb objects support also the filter framework of the mirtarbasedb (and ensembdb) package and thus allow to perform more fine-grained queries to retrieve data.

Usage

## S4 method for signature 'MirtarbaseDb'
columns(x)
## S4 method for signature 'MirtarbaseDb'
keys(x, keytype, filter,...)
## S4 method for signature 'MirtarbaseDb'
keytypes(x)

## S4 method for signature 'MirtarbaseDb'
select(x, keys, columns, keytype, ...)

Arguments

(In alphabetic order)

columns	For select: the columns from which values should be retrieved. Use the columns method to list all possible columns.
keys	The keys/ids for which data should be retrieved from the database. This can be either a character vector of keys/IDs, a single filter object extending AnnotationFilter or a list of such objects. For the latter case it is possible to combine filters and thus perform more specific queries.
keytype	For select: the type (column) that matches the provided keys. This argument does not have to be specified if argument keys is a filter object extending AnnotationFilter or a list of such objects. For keys: which keys should be returned from the database.
filter	For keys: either a single object extending AnnotationFilter or a list of such object to retrieve only specific keys from the database.

x	The MirtarbaseDb object.
...	Not used.

Value

See method description above.

Methods and Functions

columns

List all the columns that can be retrieved by the select methods. Note that these column names are different from the ones supported by the mtis method. These can be listed by the listColumns method.

Returns a character vector of supported column names.

keys

Retrieves all keys from the column name specified with keytype. By default (if keytype is not provided) it returns all Mirtarbase IDs.

Returns a character vector of IDs.

keytypes

List all supported key types (column names).

Returns a character vector of key types.

select

Retrieve the data as a data.frame based on parameters for selected keys, columns and keytype arguments. Multiple matches of the keys are returned in one row for each possible match. Argument keys can be either a character vector of keys/IDs, a single filter object extending AnnotationFilter or a list of such objects. For the latter, the argument keytype does not have to be specified.

Returns a data.frame with the column names corresponding to the argument columns and rows with all data matching the criteria specified with keys.

Author(s)

Johannes Rainer

See Also

MirtarbaseIdFilter listColumns mtis

Examples

library(mirtarbase)

## List all supported keytypes.
keytypes(mirtarbase)

## List all supported columns for the select method.
columns(mirtarbase)

## List /real/ database column names.
listColumns(mirtarbase)

## Retrieve all keys corresponding to Mirtarbase IDs.
mtiids <- keys(mirtarbase, keytype="MIRTARBASEID")
length(mtiids)
head(mtiids)

## Retrieve all keys corresponding to gene names/symbol for which we do have
## a MTI of support type "Functional MTI"
syms <- keys(mirtarbase, keytype="SYMBOL", filter=SupportTypeFilter("Functional MTI"))
length(syms)
head(syms)

## select:
## Retrieve all MTIs for the selected genes and support type.
select(mirtarbase, keys=list(GenenameFilter(c("BCL2", "BCL2L11")),
                             SupportTypeFilter("Functional MTI")),
       columns=c("SYMBOL", "MATMIRNA", "PMID"))

jotsetung/mirtarbase documentation built on May 19, 2019, 9:42 p.m.