translateMiRNAName: Translate miRNA name

In miRNAmeConverter: Convert miRNA Names to Different miRBase Versions

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)

Example output

Loading required package: miRBaseVersions.db
                    mimat        input           v15.0           v16.0
MIMAT0000431 MIMAT0000431  hsa-miR-140  hsa-miR-140-5p  hsa-miR-140-5p
MIMAT0000443 MIMAT0000443 hsa-miR-125a hsa-miR-125a-5p hsa-miR-125a-5p
                       v20.0           v21.0
MIMAT0000431  hsa-miR-140-5p  hsa-miR-140-5p
MIMAT0000443 hsa-miR-125a-5p hsa-miR-125a-5p
$names
[1] "mimat" "input" "v15.0" "v16.0" "v20.0" "v21.0"

$row.names
[1] "MIMAT0000431" "MIMAT0000443"

$class
[1] "data.frame"

$description
              input.miRNA information
hsa-miR-125a hsa-miR-125a          OK
hsa-miR-140   hsa-miR-140          OK

$sequence
                    mimat        input                    v15.0
MIMAT0000431 MIMAT0000431  hsa-miR-140   CAGUGGUUUUACCCUAUGGUAG
MIMAT0000443 MIMAT0000443 hsa-miR-125a UCCCUGAGACCCUUUAACCUGUGA
                                v16.0                    v20.0
MIMAT0000431   CAGUGGUUUUACCCUAUGGUAG   CAGUGGUUUUACCCUAUGGUAG
MIMAT0000443 UCCCUGAGACCCUUUAACCUGUGA UCCCUGAGACCCUUUAACCUGUGA
                                v21.0
MIMAT0000431   CAGUGGUUUUACCCUAUGGUAG
MIMAT0000443 UCCCUGAGACCCUUUAACCUGUGA

miRNAmeConverter documentation built on Nov. 8, 2020, 5:36 p.m.