conversion-functions: Conversion between various miRNA identifiers

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

Description

These functions use the mirbase.db package to perform conversions between miRNA identifiers (miRNA name/id to miRNA accession number) or to retrieve mature miRNAs for pre-miRNAs etc.

Usage

matmirna2matmirnaAcc( x, condition="=", ifnotfound=NA, return.type="data.frame" )
matmirna2mirfam( x, condition="=", ifnotfound=NA, return.type="data.frame" )
matmirna2mirfamAcc( x, condition="=", ifnotfound=NA, return.type="data.frame" )
matmirna2premirna( x, condition="=", ifnotfound=NA, return.type="data.frame" )
matmirna2premirnaAcc( x, condition="=", ifnotfound=NA, return.type="data.frame" )
matmirnaAcc2matmirna( x, condition="=", ifnotfound=NA, return.type="data.frame" )
matmirnaAcc2mirfam( x, condition="=", ifnotfound=NA, return.type="data.frame" )
matmirnaAcc2mirfamAcc( x, condition="=", ifnotfound=NA, return.type="data.frame" )
matmirnaAcc2premirna( x, condition="=", ifnotfound=NA, return.type="data.frame" )
matmirnaAcc2premirnaAcc( x, condition="=", ifnotfound=NA, return.type="data.frame" )

mirfam2matmirna( x, condition="=", ifnotfound=NA, return.type="data.frame" )
mirfam2matmirnaAcc( x, condition="=", ifnotfound=NA, return.type="data.frame" )
mirfam2mirfamAcc( x, condition="=", ifnotfound=NA, return.type="data.frame" )
mirfam2premirna( x, condition="=", ifnotfound=NA, return.type="data.frame" )
mirfam2premirnaAcc( x, condition="=", ifnotfound=NA, return.type="data.frame" )
mirfamAcc2matmirna( x, condition="=", ifnotfound=NA, return.type="data.frame" )
mirfamAcc2matmirnaAcc( x, condition="=", ifnotfound=NA, return.type="data.frame" )
mirfamAcc2mirfam( x, condition="=", ifnotfound=NA, return.type="data.frame" )
mirfamAcc2premirna( x, condition="=", ifnotfound=NA, return.type="data.frame" )
mirfamAcc2premirnaAcc( x, condition="=", ifnotfound=NA, return.type="data.frame" )

premirna2matmirna( x, condition="=", ifnotfound=NA, return.type="data.frame" )
premirna2matmirnaAcc( x, condition="=", ifnotfound=NA, return.type="data.frame" )
premirna2mirfam( x, condition="=", ifnotfound=NA, return.type="data.frame" )
premirna2mirfamAcc( x, condition="=", ifnotfound=NA, return.type="data.frame" )
premirna2premirnaAcc( x, condition="=", ifnotfound=NA, return.type="data.frame" )
premirnaAcc2matmirna( x, condition="=", ifnotfound=NA, return.type="data.frame" )
premirnaAcc2matmirnaAcc( x, condition="=", ifnotfound=NA, return.type="data.frame" )
premirnaAcc2mirfam( x, condition="=", ifnotfound=NA, return.type="data.frame" )
premirnaAcc2mirfamAcc( x, condition="=", ifnotfound=NA, return.type="data.frame" )
premirnaAcc2premirna( x, condition="=", ifnotfound=NA, return.type="data.frame" )

Arguments

x	a character vector or a single identifier.
condition	The condition to search for the values. Allowed are: "=", "!=", "like" and "not like", but in most cases the default ("=") is the most meaningful condition.
ifnotfound	Value to be returned if nothing was found for x.
return.type	Whether the returned object should be a data.frame (return.type="data.frame") or a list (return.type="list").

Details

These function retrieve informations from the mirbase.db Bioconductor package.

Value

A data.frame with two columns, the first containing the query, the second the values, or a list of values with the names of the elements corresponding to the query.

Author(s)

Johannes Rainer

Examples

## pre-miRNA to mature miRNA
Res <- premirna2matmirna( c( "bla", "hsa-mir-16-1", "hsa-mir-15b", "hsa-mir-16-2" ), return.type="list" )
Res
Res <- premirna2matmirnaAcc( c( "hsa-mir-15b" ) )
Res
Res <- premirnaAcc2matmirna( c( "MI0000070" ) )
Res
Res <- premirnaAcc2matmirnaAcc( c( "MI0000070" ) )
Res
Res <- premirna2premirnaAcc( "hsa-mir-15b" )
Res
Res <- premirnaAcc2premirna( "MI0000070" )
Res

## mature miRNA to pre-miRNA
Res <- matmirna2premirna( c( "hsa-miR-16-5p", "hsa-miR-16-3p" ) )
Res
Res <- matmirna2premirnaAcc( c( "hsa-miR-16-5p", "hsa-miR-16-3p" ) )
Res
Res <- matmirnaAcc2premirna( c( "MIMAT0000069", "MIMAT0004489" ) )
Res
Res <- matmirnaAcc2premirnaAcc( "MIMAT0004489" )
Res
Res <- matmirna2matmirnaAcc( "hsa-miR-16-5p" )
Res
Res <- matmirnaAcc2matmirna( "MIMAT0004489" )
Res

## pre-miRNA to mirfam and vice versa
Res <- premirna2mirfam( c( "hsa-mir-16-1", "hsa-mir-15b", "hsa-mir-16-2" ) )
Res
Res <- premirnaAcc2mirfam( "MI0000070" )
Res
Res <- mirfam2premirna( "mir-15" )
head( Res )
Res <- mirfam2premirnaAcc( "mir-15" )
head( Res )
Res <- mirfam2mirfamAcc( "mir-15" )
Res
Res <- mirfamAcc2mirfam( "MIPF0000006" )
Res
Res <- mirfamAcc2premirna( "MIPF0000006" )
head( Res )


## mature miRNAs to mirfam and vice versa
Res <- matmirna2mirfam( "hsa-miR-15b-5p" )
Res
Res <- matmirna2mirfamAcc( c( "bla", "hsa-miR-15b-5p" ) )
Res
Res <- mirfam2matmirna( "mir-15" )
head( Res )
Res <- mirfamAcc2matmirna( "MIPF0000006" )
head( Res )
Res <- mirfam2matmirnaAcc( "mir-15" )
head( Res )

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