inst/vignettes/miRNAmeConverter-vignette.R

In StefanHaunsberger/miRNAmeConverter: Convert miRNA Names to Different miRBase Versions

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library(miRNAmeConverter)

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citation("miRNAmeConverter")

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ls("package:miRNAmeConverter");

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slotNames("MiRNANameConverter");

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MiRNANameConverter();

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miRNAs = c("hsa-miR-422b", "mmu-mir-872", "gra-miR157b", "cel-miR-56*");

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nc = MiRNANameConverter();

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checkMiRNAName(nc, miRNAs);

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# "RNU-6" and "bpcv1-miR-B23" are not valid
miRNAs = c("hsa-miR-422b", "RNU-6", "mmu-miR-872", "gra-miR157b", "bpcv1-miR-B23", "bpcv1-miR-B1");
nc = MiRNANameConverter();    # Create MiRNANameConverter object
checkMiRNAName(nc, miRNAs);   # check names

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nc = MiRNANameConverter();             # Create MiRNANameConverter object
assessVersion(nc, example.miRNAs);     # Assess most likely miRBase version

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miRNA.paper = "hsa-miR-422b";
nc = MiRNANameConverter();             # Create MiRNANameConverter object
translateMiRNAName(nc, miRNA.paper);   # Translate miRNA names

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miRNAs = c("hsa-miR-128b", "hsa-miR-213", "mmu-miR-302b*", 
           "mmu-miR-872", "ebv-miR-BART5", "bpcv1-miR-B23");
nc = MiRNANameConverter();              # Create MiRNANameConverter object
result = translateMiRNAName(            # Translate names
                            nc
                            ,miRNAs
                            ,sequenceFormat = 1
                            ,versions = c(8, 8.1, 18, 21)
                            );        

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result;

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attr(result, 'description');

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attr(result, 'sequence');

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result = translateMiRNAName(            # Translate names
                            nc
                            ,miRNAs
                            ,sequenceFormat = 2
                            ,versions = c(17, 19, 21)
                            );
attr(result, 'sequence');

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#  saveResults(nc, result);

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nc = MiRNANameConverter();   # Create MiRNANameConverter object
currentVersion(nc);          # Receive the maximum miRBase version included in the package
validVersions(nc);           # Receive all valid versions
nOrganisms(nc);              # Number of organisms
validOrganisms(nc);          # Valid organisms