miRNAmeConverter (version 1.0.2)

translateMiRNAName: Translate miRNA name

Description

This function translates input miRNA names to different miRBase versions.

Usage

translateMiRNAName(this, miRNAs, versions, current = FALSE, verbose = FALSE)
## S3 method for class 'MiRNANameConverter,character':
translateMiRNAName(this, miRNAs,
  versions, current = FALSE, 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

current

A boolean telling if also the current miRBase version shall be returned

verbose

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

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).

Methods (by class)

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

Details

This is 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

See Also

attr for attributes

Examples

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