| Title: | A comprehensive and high-efficiency tool for converting and retrieving the information of miRNAs in different miRBase versions |
|---|---|
| Description: | A comprehensive tool for converting and retrieving the miRNA Name, Accession, Sequence, Version, History and Family information in different miRBase versions. It can process a huge number of miRNAs in a short time without other depends. |
| Authors: | Taosheng Xu<[email protected]>, Thuc Le<[email protected]> |
| Maintainer: | Taosheng Xu<[email protected]> |
| License: | GPL (>= 2) |
| Version: | 1.29.0 |
| Built: | 2024-07-24 04:29:14 UTC |
| Source: | https://github.com/bioc/miRBaseConverter |
This function checks the miRNA status (Alive or Dead) in the latest miRBase version.
checkMiRNAAlive(Accessions, verbose = TRUE)checkMiRNAAlive(Accessions, verbose = TRUE)
Accessions |
A character vector representing the miRNA Accessions in miRBase. |
verbose |
Logical value. If true, the dead miRNAs will be printed the console. |
A character vector of Accessions for all alive miRNAs. The names of the return vector are the position indexes in the input Accessions.
Xu, Taosheng [email protected]
data(miRNATest) ## The input is miRNA Accessions Accessions=miRNATest$Accession alive_Accession1=checkMiRNAAlive(Accessions) ##The input is miRNA names miRNANames=miRNATest$miRNA_Name version=checkMiRNAVersion(miRNANames,verbose = TRUE) result=miRNA_NameToAccession(miRNANames,version = version) Accessions=result$Accession alive_Accession2=checkMiRNAAlive(Accessions)data(miRNATest) ## The input is miRNA Accessions Accessions=miRNATest$Accession alive_Accession1=checkMiRNAAlive(Accessions) ##The input is miRNA names miRNANames=miRNATest$miRNA_Name version=checkMiRNAVersion(miRNANames,verbose = TRUE) result=miRNA_NameToAccession(miRNANames,version = version) Accessions=result$Accession alive_Accession2=checkMiRNAAlive(Accessions)
This function checks the miRNA family for a list of miRNA Names.
checkMiRNAFamily(Accessions)checkMiRNAFamily(Accessions)
Accessions |
A character vector representing the miRNA Accessions in miRBase. |
A data frame with four columns. The number of rows equal to the input Accessions. The four columns are defined as below:
Accession : The input miRNA accessions.
miRNAName_v21 : The miRNA names (version 21) corresponding to the Accession.
FamilyAccession : The accession of the family .
Family : The family name.
Xu, Taosheng [email protected]
data(miRNATest) ## The input is miRNA Accessions Accessions=miRNATest$Accession Family_Info1=checkMiRNAFamily(Accessions) ##The input is miRNA names miRNANames=miRNATest$miRNA_Name version=checkMiRNAVersion(miRNANames,verbose = TRUE) result=miRNA_NameToAccession(miRNANames,version=version) Accessions=result$Accession Family_Info2=checkMiRNAFamily(Accessions)data(miRNATest) ## The input is miRNA Accessions Accessions=miRNATest$Accession Family_Info1=checkMiRNAFamily(Accessions) ##The input is miRNA names miRNANames=miRNATest$miRNA_Name version=checkMiRNAVersion(miRNANames,verbose = TRUE) result=miRNA_NameToAccession(miRNANames,version=version) Accessions=result$Accession Family_Info2=checkMiRNAFamily(Accessions)
This function checks the most possible miRBase version for a list of miRNA names.
checkMiRNAVersion(miRNANames, verbose = TRUE)checkMiRNAVersion(miRNANames, verbose = TRUE)
miRNANames |
A character vector representing the miRNA names. |
verbose |
Logical value. If true, the detail version information is printed in the console for user reference. |
A single character value or a character vector represent the most possible miRBase version for the list of miRNA names.
Xu, Taosheng [email protected]
data(miRNATest) miRNANames=miRNATest$miRNA_Name version=checkMiRNAVersion(miRNANames,verbose=TRUE)data(miRNATest) miRNANames=miRNATest$miRNA_Name version=checkMiRNAVersion(miRNANames,verbose=TRUE)
This function gets all miRNAs in the specified miRBase version.
getAllMiRNAs(version = "v22", type = "all", species = "all")getAllMiRNAs(version = "v22", type = "all", species = "all")
version |
A character value representing the specified miRBase version for
retrieval. Users can apply the function getAllVersionInfo() to get the available miRNA version names.
The optional values are in below: |
type |
A character value representing the miRNA type for retrieval.
|
species |
A character value representing the abbreviation of species. Users can apply the getAllSpecies() function to get the available abbreviation of species. If species is set to "all", the miRNAs of all species will return. |
A data frame with three columns. The three columns are defined as below:
Accession
Name
Sequence
Xu, Taosheng [email protected]
miRNAs=getAllMiRNAs(version="v22", type="all", species="hsa")miRNAs=getAllMiRNAs(version="v22", type="all", species="hsa")
This function return a reference for all species of miRNAs including the abbreviation and full name.
getAllSpecies()getAllSpecies()
A dataframe A data frame with two columns. The two columns are defined as below:
Species
FullName
Xu, Taosheng [email protected]
allSpecies=getAllSpecies()allSpecies=getAllSpecies()
This function return a reference for all miRBase versions' information including Version name, Release date, miRNA number and Status.
getAllVersionInfo()getAllVersionInfo()
The detailed version information is printed in the console for user reference.
Xu, Taosheng [email protected]
getAllVersionInfo()getAllVersionInfo()
This function returns all available miRBase versions' information of a single specified miRNA.
getMiRNAHistory(Accession)getMiRNAHistory(Accession)
Accession |
A character representing the single Accession. |
A data frame including all the history information (Precursor, Mature, Sequence) of the specified miRNA. Each row represents a miRBase version.
Xu, Taosheng [email protected]
#####1,The input is a miRNA Name miRNAName="hsa-miR-26b-5p" result1=miRNA_NameToAccession(miRNAName,version="v22") Accession=result1$Accession result2=getMiRNAHistory(Accession) #####2,The input is miRNA Accession Accession="MIMAT0000765" result3=getMiRNAHistory(Accession)#####1,The input is a miRNA Name miRNAName="hsa-miR-26b-5p" result1=miRNA_NameToAccession(miRNAName,version="v22") Accession=result1$Accession result2=getMiRNAHistory(Accession) #####2,The input is miRNA Accession Accession="MIMAT0000765" result3=getMiRNAHistory(Accession)
This function returns the miRNA sequences for a list of miRNAs.
getMiRNASequence(Accessions, targetVersion = "v22")getMiRNASequence(Accessions, targetVersion = "v22")
Accessions |
A character vector representing the miRNA Accessions in miRBase. |
targetVersion |
A character value representing the target miRBase version corresponding the Accessions.
Users can apply the function getAllVersionInfo() to get the available miRNA version names.
The optional values are in below: |
A nx2 data frame. The number of row equals to input miRNAs. The two columns are defined as below:
Accession : The original miRNA (Column 1).
miRNASequence_{targetVersion} : The return miRNA sequence (in specified version) corresponding to the input miRNAs (Column 2).
Xu, Taosheng [email protected]
#####1, The input are miRNA Accessions data(miRNATest) Accessions=miRNATest$Accession result1=getMiRNASequence(Accessions,targetVersion="v13") result2=getMiRNASequence(Accessions,targetVersion="v22") #####2, The input are miRNA Names data(miRNATest) miRNANames=miRNATest$miRNA_Name result3=miRNAVersionConvert(miRNANames,targetVersion="v22",exact=TRUE) Accessions=result3$Accession result4=getMiRNASequence(Accessions,targetVersion="v22")#####1, The input are miRNA Accessions data(miRNATest) Accessions=miRNATest$Accession result1=getMiRNASequence(Accessions,targetVersion="v13") result2=getMiRNASequence(Accessions,targetVersion="v22") #####2, The input are miRNA Names data(miRNATest) miRNANames=miRNATest$miRNA_Name result3=miRNAVersionConvert(miRNANames,targetVersion="v22",exact=TRUE) Accessions=result3$Accession result4=getMiRNASequence(Accessions,targetVersion="v22")
This function returns the full miRNAs information table of the specified miRBase version
getMiRNATable(version = "v22", species = "all")getMiRNATable(version = "v22", species = "all")
version |
A character value representing the specified miRBase version for
retrieval. Users can apply the function getAllVersionInfo() to get the available miRNA version names.
The optional values are in below: |
species |
A character value representing the abbreviation of species. Users can apply the function getAllSpecies() to get the available abbreviation of species. If species is set to "all", the miRNAs of all species will return. |
A data frame
Xu, Taosheng [email protected]
miRNA_Tab=getMiRNATable(version="v22",species="hsa")miRNA_Tab=getMiRNATable(version="v22",species="hsa")
This function redirects the miRBase webpage of the specified miRNAs
goTo_miRBase(Accessions)goTo_miRBase(Accessions)
Accessions |
A character vector representing the miRNA Accessions in miRBase. We restict the number of queried miRNAs each time. The maximum number of the input miRNAs is 15. |
No values
Xu, Taosheng [email protected]
#### 1. A step-loop Accession1="MI0000447" goTo_miRBase(Accession1) #### 2. A mature miRNA Accession2="MIMAT0026477" goTo_miRBase(Accession2) #### 3. A list of miRNAs Accession3=miRNATest$Accession[1:10] goTo_miRBase(Accession3)#### 1. A step-loop Accession1="MI0000447" goTo_miRBase(Accession1) #### 2. A mature miRNA Accession2="MIMAT0026477" goTo_miRBase(Accession2) #### 3. A list of miRNAs Accession3=miRNATest$Accession[1:10] goTo_miRBase(Accession3)
This function redirects the miRBase miRNA family webpages of the specified miRNA families
goTo_miRNAFamily(FamilyAccessions, verbose = TRUE)goTo_miRNAFamily(FamilyAccessions, verbose = TRUE)
FamilyAccessions |
A character vector representing the miRNA family Accessions in miRBase. We restict the queried number of miRNA family each time. The maximum number of the input miRNA families is 15. |
verbose |
Logical value. If true, the invalid miRNA Family will be printed the console. |
No values
Xu, Taosheng [email protected]
data(miRNATest) Accessions=miRNATest$Accession Family_Info=checkMiRNAFamily(Accessions) FamilyAccessions=Family_Info$FamilyAccession[1:15] goTo_miRNAFamily(FamilyAccessions)data(miRNATest) Accessions=miRNATest$Accession Family_Info=checkMiRNAFamily(Accessions) FamilyAccessions=Family_Info$FamilyAccession[1:15] goTo_miRNAFamily(FamilyAccessions)
This function converts a group of any species' miRNA Accessions (including precursor and mature miRNA) to a specified miRBase version if the Accessions have been defined in miRBase.
miRNA_AccessionToName(Accessions, targetVersion = "v22")miRNA_AccessionToName(Accessions, targetVersion = "v22")
Accessions |
A character vector representing the miRNA Accessions needed to be convert. |
targetVersion |
A character value representing the target miRBase version corresponding the Accessions.
The optional values are in below: |
A nx2 data frame. The number of rows equal to the input miRNA names. The two columns are defined as below:
Accession : The Accession of miRNAs (Column 1).
TargetName : The converted miRBase names (in specified version) corresponding to the Accessions (Column 2).
Xu, Taosheng [email protected]
data(miRNATest) Accessions=miRNATest$Accession result1=miRNA_AccessionToName(Accessions,targetVersion="v13") result2=miRNA_AccessionToName(Accessions,targetVersion="v22")data(miRNATest) Accessions=miRNATest$Accession result1=miRNA_AccessionToName(Accessions,targetVersion="v13") result2=miRNA_AccessionToName(Accessions,targetVersion="v22")
This function converts the mature miRNAs to the corresponding precursors in the specified miRBase version.
miRNA_MatureToPrecursor(miRNANames, version = NULL)miRNA_MatureToPrecursor(miRNANames, version = NULL)
miRNANames |
A character vector representing the miRNA names. |
version |
The default is NULL representing the most possible latest version of the input miRNA Names will be checked automatically.
Otherwise, a character value representing the version corresponding the input miRNA Names.
Users can apply the function getAllVersionInfo() to get the available miRNA version names.
The optional values are in below: |
A data frame(nx2). The number of rows equal to the input miRNA Names. The two columns are defined as below:
OriginalName : The input miRNA Names.
Precursor : The corresponding precursors of the mature miRNAs.
Xu, Taosheng [email protected]
data(miRNATest) miRNANames=miRNATest$miRNA_Name result=miRNA_MatureToPrecursor(miRNANames)data(miRNATest) miRNANames=miRNATest$miRNA_Name result=miRNA_MatureToPrecursor(miRNANames)
This function converts a group of any species' miRNA name to the Accessions defined in miRBase.
miRNA_NameToAccession(miRNANames, version = "v22")miRNA_NameToAccession(miRNANames, version = "v22")
miRNANames |
A character vector representing the source miRNA names needed to be convert. |
version |
A character value representing the version corresponding the miRNANames.
Users can apply the function getAllVersionInfo() to get the available miRNA version names.
The optional values are in below: |
A nx2 data frame. The number of rows equal to the input miRNA names. The two columns are defined as below:
miRNAName_{Version} : The input miRNA names (Column 1).
Accession : The convert Accession(Column 2).
Xu, Taosheng [email protected]
data(miRNATest) miRNANames=miRNATest$miRNA_Name version=checkMiRNAVersion(miRNANames,verbose=TRUE) result1=miRNA_NameToAccession(miRNANames,version=version) result2=miRNA_AccessionToName(result1[,2],targetVersion="v22") result3=miRNAVersionConvert(miRNANames,targetVersion="v22",exact=TRUE)data(miRNATest) miRNANames=miRNATest$miRNA_Name version=checkMiRNAVersion(miRNANames,verbose=TRUE) result1=miRNA_NameToAccession(miRNANames,version=version) result2=miRNA_AccessionToName(result1[,2],targetVersion="v22") result3=miRNAVersionConvert(miRNANames,targetVersion="v22",exact=TRUE)
This function converts the precursors to the corresponding mature miRNAs in the specified miRBase version.
miRNA_PrecursorToMature(miRNANames, version = NULL)miRNA_PrecursorToMature(miRNANames, version = NULL)
miRNANames |
A character vector representing the miRNA names. |
version |
The default is NULL representing the most possible latest version of the input miRNA Names will be checked automatically.
Otherwise, a character value representing the version corresponding the input miRNA Names.
Users can apply the function getAllVersionInfo() to get the available miRNA version names.
The optional values are in below: |
A data frame(nx3). The number of rows equal to the input miRNA names. The three columns are defined as below:
OriginalName : The input miRNA Names.
Mature1 : The corresponding mature miRNAs (always "-5p") .
Mature2 : The corresponding mature miRNAs (always "-3p") .
If the input miRNA Names mingle mature miRNA names, the mature miRNA names will match to themselves in the output.
Xu, Taosheng [email protected]
miRNANames=c("pma-mir-100a","sko-mir-92a","hsa-mir-6131","mtr-MIR2655i", "mmu-mir-153","mtr-MIR2592am","mml-mir-1239","xtr-mir-128-2","oan-mir-100", "mmu-mir-378b","hsa-miR-508-5p","mmu-miR-434-3p") result=miRNA_PrecursorToMature(miRNANames)miRNANames=c("pma-mir-100a","sko-mir-92a","hsa-mir-6131","mtr-MIR2655i", "mmu-mir-153","mtr-MIR2592am","mml-mir-1239","xtr-mir-128-2","oan-mir-100", "mmu-mir-378b","hsa-miR-508-5p","mmu-miR-434-3p") result=miRNA_PrecursorToMature(miRNANames)
Accession : miRNA Accessions in miRBase
miRNA_Name : miRNA names
A data frame
This is a mixed miRNA name collection of some species for the examples' test in the package.
data(miRNATest)data(miRNATest)
This function converts a group of any species' miRNA names (including precursor and mature miRNA) to the specified miRBase version if the miRNAs have been defined in miRBase.
miRNAVersionConvert( miRNANames, targetVersion = "v22", exact = TRUE, verbose = TRUE )miRNAVersionConvert( miRNANames, targetVersion = "v22", exact = TRUE, verbose = TRUE )
miRNANames |
A character vector representing the source miRNA names needed to be convert. |
targetVersion |
A character value representing the target miRBase version corresponding the source miRNA names.
Users can apply the function getAllVersionInfo() to get the available miRNA version names.
The optional values are in below: |
exact |
Logical value. If true, the result will be the most exactly matched result. If FALSE, the result will include all the possible matched miRNA name. If one miRNA can match multiple names. All the matched names are concatenated with "&". |
verbose |
Logical value. If true, it will print the multiple matched miRNA Names and Accessions to the console. |
A data frame with three columns. The number of rows equal to the input miRNA names. The three columns are defined as below:
OriginalName : The original miRNA names (Column 1).
TargetName : The converted miRBase names (in specified version) corresponding to the original miRNA names (Column 2).
Accession : The corresponding miRBase Accessions (Column 3).
Please note: Due to some miRNA names changing many times in history. Even if choose the third parameter "exact"=TRUE, it may still have some miRNAs that can't match the unique name in the target version. In order to return the accurate result as possible, we also concatenate the multiple matched miRNA names with "&". This is the rare case but it happens sometimes.
Xu, Taosheng [email protected]
data(miRNATest) miRNANames=miRNATest$miRNA_Name result1=miRNAVersionConvert(miRNANames,targetVersion="v13",exact=TRUE,verbose=TRUE) result2=miRNAVersionConvert(miRNANames,targetVersion="v22",exact=TRUE,verbose=TRUE) result3=miRNAVersionConvert(miRNANames,targetVersion="v22",exact=FALSE,verbose=TRUE) miRNANames=c( "hsa-let-7c","hsa-miR-3190-3p","hsa-let-7c","hsa-miR-34b","hsa-miR-378", "hsa-miR-499a-3p","hsa-miR-499a-5p","hsa-miR-500","hsa-miR-516a-5p","hsa-miR-550","hsa-miR-589") result4=miRNAVersionConvert(miRNANames, targetVersion="v22", exact=TRUE, verbose=TRUE)data(miRNATest) miRNANames=miRNATest$miRNA_Name result1=miRNAVersionConvert(miRNANames,targetVersion="v13",exact=TRUE,verbose=TRUE) result2=miRNAVersionConvert(miRNANames,targetVersion="v22",exact=TRUE,verbose=TRUE) result3=miRNAVersionConvert(miRNANames,targetVersion="v22",exact=FALSE,verbose=TRUE) miRNANames=c( "hsa-let-7c","hsa-miR-3190-3p","hsa-let-7c","hsa-miR-34b","hsa-miR-378", "hsa-miR-499a-3p","hsa-miR-499a-5p","hsa-miR-500","hsa-miR-516a-5p","hsa-miR-550","hsa-miR-589") result4=miRNAVersionConvert(miRNANames, targetVersion="v22", exact=TRUE, verbose=TRUE)