miRNAVersionConvert: miRBase version convert for miRNA Names

In miRBaseConverter: A comprehensive and high-efficiency tool for converting and retrieving the information of miRNAs in different miRBase versions

Description

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.

Usage

miRNAVersionConvert(miRNANames, targetVersion = "v22", exact = TRUE,
  verbose = TRUE)

Arguments

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: "v6","v7_1","v8","v8_1","v8_2","v9","v9_1","v9_2","v10","v10_1","v11","v12","v13","v14", "v15","v16","v17","v18","v19","v20","v21","v22"
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.

Value

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).

Note

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.

Author(s)

Xu, Taosheng [e-mail]

Examples

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)

Example output

********************************************

The multiple matched miRNAs are list below: 

    original           Version v13              Accession
1 hsa-let-7c hsa-let-7c&hsa-let-7c MI0000064&MIMAT0000064
2  cel-lsy-6   cel-lsy-6&cel-lsy-6 MI0000801&MIMAT0000749
********************************************

The multiple matched miRNAs are list below: 

       original                  Version v22                 Accession
1  mtr-miR2111f    mtr-miR2111k&mtr-miR2111f MIMAT0013361&MIMAT0021256
2    hsa-let-7c     hsa-let-7c&hsa-let-7c-5p    MI0000064&MIMAT0000064
3  mtr-miR2111j mtr-miR2111d-5p&mtr-miR2111j MIMAT0013291&MIMAT0013360
4  mtr-miR2111h    mtr-miR2111c&mtr-miR2111h MIMAT0013289&MIMAT0013295
5   mtr-miR169j      mtr-miR169b&mtr-miR169j MIMAT0011111&MIMAT0013321
6  mtr-miR2111c    mtr-miR2111c&mtr-miR2111b MIMAT0013289&MIMAT0013358
7  mtr-miR2111o    mtr-miR2111i&mtr-miR2111o MIMAT0013296&MIMAT0013300
8  mtr-miR2111n    mtr-miR2111h&mtr-miR2111n MIMAT0013295&MIMAT0013299
9     cel-lsy-6       cel-lsy-6&cel-lsy-6-3p    MI0000801&MIMAT0000749
10 mtr-miR2111k mtr-miR2111e-5p&mtr-miR2111k MIMAT0013292&MIMAT0013361
********************************************

The multiple matched miRNAs are list below: 

     original                     Version v22                 Accession
1 hsa-miR-34b   hsa-miR-34b-5p&hsa-miR-34b-3p MIMAT0000685&MIMAT0004676
2 hsa-miR-378 hsa-miR-378a-5p&hsa-miR-378a-3p MIMAT0000731&MIMAT0000732
3 hsa-miR-500 hsa-miR-500a-3p&hsa-miR-500a-5p MIMAT0002871&MIMAT0004773
4 hsa-miR-550 hsa-miR-550a-3p&hsa-miR-550a-5p MIMAT0003257&MIMAT0004800
5 hsa-miR-589   hsa-miR-589-3p&hsa-miR-589-5p MIMAT0003256&MIMAT0004799

miRBaseConverter documentation built on Nov. 8, 2020, 11:08 p.m.