Package 'miRNAmeConverter'

Title: Convert miRNA Names to Different miRBase Versions
Description: Translating mature miRNA names to different miRBase versions, sequence retrieval, checking names for validity and detecting miRBase version of a given set of names (data from http://www.mirbase.org/).
Authors: Stefan Haunsberger [aut, cre]
Maintainer: Stefan J. Haunsberger <[email protected]>
License: Artistic-2.0
Version: 1.35.0
Built: 2024-10-30 08:47:53 UTC
Source: https://github.com/bioc/miRNAmeConverter

Help Index

Check if given miRNA names can be assigned to unique MIMAT accessions among all versions

Description

This function checks if the names from a given set of mature miRNAs have a unique MIMAT ID. Check if given miRNA names can be assigned to unique MIMAT accessions among all versions

This function checks if the names from a given set of mature miRNAs have a unique MIMAT ID.

Usage

assessMiRNASwappingMIMAT(this, miRNAs, verbose = FALSE)

Arguments

this

Object of class 'MiRNANameConverter'
miRNAs

A character vector of miRNA names
verbose

A boolean to either show more (TRUE) or less information (FALSE)

Details

Although the majority of miRNA names can be assigned to a unique MIMAT ID (accession) some miRNAs changed MIMAT ID in different versions. This function takes the input miRNA names and checks each one of them if they have a unique MIMAT ID over all versions. If a miRNA changes MIMAT ID in a version it will be comprised in the return vector.

Value

A character vector containing miRNA names that do not have a unique MIMAT ID

Author(s)

Stefan Haunsberger

Assess miRBase version

Description

This function detects the most likely miRBase version of a given miRNA set. Assess miRBase version

This function detects the most likely miRBase version of a given miRNA set.

Usage

assessVersion(this, miRNAs, verbose = FALSE)

## S4 method for signature 'MiRNANameConverter'
assessVersion(this, miRNAs, verbose = FALSE)

Arguments

this

Object of class 'MiRNANameConverter'
miRNAs

A character vector of miRNA names
verbose

A boolean to either show more (TRUE) or less information (FALSE)

Details

This function takes a set of miRNA names and detects the most likely miRBase version of this given set of 'miRNAs'. First all miRNAs will be checked for validity (if they are actual miRNA names checkMiRNAName and the set that passes the check will be further processed.

Value

A data frame with two columns: version and frequency (decreasing order by frequency, version) + version: miRBase version + frequency: the number of valid miRNAs that could be assigned to the version respectively

Methods (by class)

  • MiRNANameConverter: Method for assessing the most likely miRBase version that a given set of miRNA names is from.

Author(s)

Stefan Haunsberger

Examples

nc = MiRNANameConverter(); # Instance of class 'MiRNANameConverter'
assessVersion(nc, miRNAs = c("hsa-miR-140", "hsa-miR-125a"))

Check miRNA names for validity

Description

This function checks for a given set of mature 'miRNAs' (names) Check miRNA names for validity

This function checks for a given set of mature 'miRNAs' (names) if the names are listed in any miRBase version respectively.

Usage

checkMiRNAName(this, miRNAs, verbose = FALSE)

## S4 method for signature 'MiRNANameConverter'
checkMiRNAName(this, miRNAs, verbose = FALSE)

Arguments

this

Object of class 'MiRNANameConverter'
miRNAs

A character vector of miRNA names
verbose

A boolean to either show more (TRUE) or less information (FALSE)

Details

This function takes the input miRNA names and checks each one of them for validity. The check is done by taking each miRNA and searches for an existing entry in the miRBase database among all versions. miRNAs that are listed in any version will be comprised in the return vector respectively. If no valid miRNA was detected, a character(0) will be returned.

Value

A character vector containing a set of valid miRNA names

Methods (by class)

  • MiRNANameConverter: Method for checking for valid miRNA names

Author(s)

Stefan Haunsberger

Examples

nc = MiRNANameConverter() # Instance of class 'MiRNANameConverter'
# Test with correct inputs
checkMiRNAName(nc, miRNAs = c("hsa-miR-29a", "hsa-miR-642"))

Get current version

Description

This function returns the highest miRBase version that is provided by the package.

Usage

currentVersion(this)

## S4 method for signature 'MiRNANameConverter'
currentVersion(this)

Arguments

this

Object of class MiRNAmeConverter

Details

The maximum miRBase version of the package is evaluated and set in the object initialization.

Value

A numeric value

Methods (by class)

  • MiRNANameConverter: Retrieve highest supported miRBase version

Author(s)

Stefan Haunsberger

Examples

nc = MiRNANameConverter(); # Instance of class 'MiRNANameConverter'
currentVersion(nc);

Set current version

Description

Set the highest version that is supported by the package.

Usage

currentVersion(this) <- value

Arguments

this

Object of class ”
value

A numeric value

Details

The value for the highest version is a static variable. It is initialized in the initialization method when an instance of a MiRNANameConverter class is created.

Value

Object of class ”

Author(s)

Stefan Haunsberger

miRNA names.

Description

Sample names including miRNA names, non-miRNA names and other. It also includes duplicates.

Usage

example.miRNAs

Format

A character vector containing names.

MiRNANameConverter constructor

Description

This function returns an instance of a MiRNANAmeConverter class. Handling mature miRNA names from different miRBase versions This package contains algorithms for dealing with mature miRNA names from different miRBase release versions. The functions are provided in form of methods as part of the MiRNANameConverter-class. The data of all the miRBase release versions is stored in the miRBaseVersions.db annotation package. The MiRNAmeConverter package contains one class that has two categories of functions: getters-functions and algorithms.

Classes

The MiRNANameConverter

Getter functions

The getter functions provide access to the slots of the class.

Algorithms

There are three algorithms for dealing with miRNA names from different miRBase releases, the assessVersion, checkMiRNAName and translateMiRNAName.

translateMiRNAName

The algorithm coded in this function can translate given miRNA names to different miRBase release versions.

checkMiRNAName

This function is used to check if a given miRNA name is listed in the current miRBase release.

assessVersion

The assessVersion

-function is useful when one wants to assess the miRBase version of a given set of mature miRNA names.

Author(s)

Stefan Haunsberger [email protected]

See Also

miRBaseVersions.db for more information about the database holding all major miRBase release versions)

Examples

# Translate a mature miRNA name to miRBase version 21.0
nc = MiRNANameConverter(); # Object instantiation
translateMiRNAName(nc, "hsa-miR-29a", version = 21.0)

Instantiate from MiRNANameConverter class

Description

This function returns back an instance of a MiRNANAmeConverter object.

Usage

MiRNANameConverter(...)

Arguments

...

any optional arguments

Slots

.dbconn

Database connection

.currentVersion

Current miRBase version

.validVersions

Valid/Supported miRBase versions

.nOrganisms

Number of different organisms supported

.nTotalEntries

Total number of mature miRNA names among all provided miRBase release versions in the miRBaseVersions.db package.

.validOrganisms

Valid organisms

Author(s)

Stefan Haunsberger

MiRNANameConverter constructor

Description

This function returns an instance of a MiRNANAmeConverter class.

Usage

## S4 method for signature 'ANY'
MiRNANameConverter()

Details

This function initializes an object of the class MiRNANameConverter. It is a wrapper for new().

Value

an object of class 'MiRNANameConverter'

Author(s)

Stefan Haunsberger

See Also

new

Examples

nc = MiRNANameConverter() # Instance of class 'MiRNANameConverter'

Get number of organisms

Description

This function returns the number of different organisms that are provided by the package.

Usage

nOrganisms(this)

## S4 method for signature 'MiRNANameConverter'
nOrganisms(this)

Arguments

this

Object of class MiRNAmeConverter

Details

The number of different organisms is evaluated and set in the object initialization.

Value

A numeric value

Methods (by class)

  • MiRNANameConverter: Retrieve number of organisms

Author(s)

Stefan Haunsberger

Examples

nc = MiRNANameConverter(); # Instance of class 'MiRNANameConverter'
nOrganisms(nc);

Set number of organisms

Description

This function sets the number of different organisms that are provided by the package.

Usage

nOrganisms(this) <- value

Arguments

this

Object of class MiRNANameConverter
value

An integer value

Details

The number of different organisms is evaluated and set in the object initialization.

Value

A MiRNANameConverter object

Author(s)

Stefan Haunsberger

Get total number database entries

Description

This function returns the total number of entries contained in the mimat table. The number is the sum of the entries of all miRBase versions provided by the package.

Usage

nTotalEntries(this)

## S4 method for signature 'MiRNANameConverter'
nTotalEntries(this)

Arguments

this

Object of class MiRNAmeConverter

Details

The total number is evaluated and set in the object initialization.

Value

A numeric value

Methods (by class)

  • MiRNANameConverter: Retrieve total number of miRNA entries

Author(s)

Stefan Haunsberger

Examples

nc = MiRNANameConverter(); # Instance of class 'MiRNANameConverter'
nTotalEntries(nc);

Set total number database entries

Description

This function sets the total number of entries contained in the mimat table. The number is the sum of the entries of all miRBase versions provided by the package.

Usage

nTotalEntries(this) <- value

Arguments

this

Object of class MiRNANameConverter
value

An integer value

Details

The total number is evaluated and set in the object initialization.

Value

A MiRNANameConverter object

Author(s)

Stefan Haunsberger

Save miRNA translation results

Description

This function saves the data frame returned from translateMiRNAName inclusive the attribute 'description'. Save miRNA translation results

This function saves the data frame returned from translateMiRNAName inclusive the attribute 'description'.

Usage

saveResults(this, df, outputFilename, outputPath, sep = "\t",
  quote = FALSE, verbose = FALSE, ...)

## S4 method for signature 'MiRNANameConverter,data.frame'
saveResults(this, df, outputFilename,
  outputPath, sep = "\t", quote = FALSE, verbose = FALSE, ...)

Arguments

this

Object of class 'MiRNANameConverter'
df

A data.frame with translated results
outputFilename

A filename for the output file, such as 'filename.txt'
outputPath

A file path (character string) to the target directory
sep

Separator
quote

If all data values shall be surrounded by ('"')
verbose

Boolean to either show more (TRUE) or less information (FALSE)
...

Arguments that can be passed on to write.table

Details

This function saves a data frame that has been returned by translateMiRNAName. The attribute 'description' of the data frame will be stored as well.

Methods (by class)

  • this = MiRNANameConverter,df = data.frame: Method for saving translation results

Author(s)

Stefan Haunsberger

See Also

write.table for additional parameter values for the '...' argument, attr for how to retrieve attributes

Examples

nc = MiRNANameConverter(); # Instance of class 'MiRNANameConverter'
res = translateMiRNAName(nc, miRNAs = c("hsa-miR-140", "hsa-miR-125a"),
                           versions = c(15, 16, 20, 21))
# Save translation results
saveResults(nc, res)

Show-method

Description

This function prints object specific information Show-method

This function prints object specific information

Usage

## S4 method for signature 'MiRNANameConverter'
show(object)

Arguments

object

Object of class MiRNANameConverter

Details

This function prints some information to the console.

Author(s)

Stefan Haunsberger

See Also

show

Translate miRNA name

Description

This function translates input miRNA names to different miRBase versions. Translate miRNA name

This function translates input miRNA names to different miRBase versions.

Usage

translateMiRNAName(this, miRNAs, versions, sequenceFormat = 1,
  verbose = FALSE)

## S4 method for signature 'MiRNANameConverter,character'
translateMiRNAName(this, miRNAs,
  versions, sequenceFormat = 1, verbose = FALSE)

Arguments

this

Object of class 'MiRNANameConverter'
miRNAs

A character vector of miRNA names
versions

An integer or numerical vector containing the target versions
sequenceFormat

Integer value indicating the return format for the data frame containing sequence information 1=only sequences, 2=miRNA name and sequence
verbose

A boolean to either show more (TRUE) or less information (FALSE)

Details

The translation and sequence retrieval are done in 5 main steps: 1) Only take miRNA names that do not swap MIMAT IDs among versions (assessMiRNASwappingMIMAT) 2) Check, if the miRNA names are valid names (checkMiRNAName) 3) Receive unique MIMAT IDs for each valid miRNA - If there are miRNAs that have basically the same name, only use miRNA names from the highest version 4) Check if the found MIMAT IDs are still listed in the current miRBase version - If not, neglect it because then it is not considered to be a miRNA anymore 5) Receive names from desired versions

Value

A (n x m) data frame where n is the number of valid miRNAs and m the number of columns (minimum 3 columns, MIMAT-ID (accession), input miRNA name, current version) In addition an attribute 'description' is added to the data frame where to each miRNA some notes are added (for example why a certain miRNA is not in the output). Sequence information is attached as the attribute 'sequence'.

Methods (by class)

  • this = MiRNANameConverter,miRNAs = character: Method for translating miRNA name(s) to different miRBase versions

Author(s)

Stefan Haunsberger

See Also

attr for attributes

Examples

nc = MiRNANameConverter(); # Instance of class 'MiRNANameConverter'
res = translateMiRNAName(nc, miRNAs = c("hsa-miR-140", "hsa-miR-125a"),
                   versions = c(15, 16, 20, 21))
res
attributes(res)

Get valid organisms

Description

This function returns all organisms where mature miRNA names are available in any of the provided miRBase versions.

Usage

validOrganisms(this)

## S4 method for signature 'MiRNANameConverter'
validOrganisms(this)

Arguments

this

Object of class MiRNAmeConverter

Details

The valid organisms are evaluated and set in the object initialization.

Value

A numeric value

Methods (by class)

  • MiRNANameConverter: Retrieve all supported organisms

Author(s)

Stefan Haunsberger

Examples

nc = MiRNANameConverter(); # Instance of class 'MiRNANameConverter'
nOrganisms(nc);

Set valid organisms

Description

This function sets all organisms where mature miRNA names are available in any of the provided miRBase versions.

Usage

validOrganisms(this) <- value

Arguments

this

Object of class MiRNANameConverter
value

A character vector

Details

The valid organisms are evaluated and set in the object initialization.

Value

A MiRNANameConverter object

Author(s)

Stefan Haunsberger

Get valid versions

Description

This function returns all valid miRBase versions provided by the package.

Usage

validVersions(this)

## S4 method for signature 'MiRNANameConverter'
validVersions(this)

Arguments

this

Object of class MiRNAmeConverter

Value

A numeric vector

Methods (by class)

  • MiRNANameConverter: Retrieve supported miRBase versions

Author(s)

Stefan Haunsberger

Examples

validVersions
nc = MiRNANameConverter(); # Instance of class 'MiRNANameConverter'
validVersions(nc);

Set valid versions

Description

Set version values that are supported by the package.

Usage

validVersions(this) <- value

Arguments

this

Object of class MiRNANameConverter
value

A vector of numeric values

Details

The value for the highest versions is a static variable. It is initialized in the initialization method when an instance of a MiRNANameConverter class is created.

Value

A MiRNANameConverter object

Author(s)

Stefan Haunsberger