## ----global_options, echo = FALSE, include = FALSE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- options(width = 999) knitr::opts_chunk$set(echo = TRUE, warning = FALSE, message = FALSE, cache = FALSE, tidy = FALSE, size = "small") ## ----setup, echo = FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- knitr::opts_chunk$set(collapse = TRUE) ## ----message = FALSE,warning = FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- library(miRBaseConverter) data(miRNATest) miRNANames = miRNATest$miRNA_Name version=checkMiRNAVersion(miRNANames, verbose = TRUE) ## ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ library(miRBaseConverter) data(miRNATest) Accessions = miRNATest$Accession #### 1. Convert to the Accessions to miRNA names in miRBase version 13 result1 = miRNA_AccessionToName(Accessions,targetVersion = "v13") result1[c(341:345),] ####2. Convert to the Accessions to miRNA names in miRBase version 22. result2 = miRNA_AccessionToName(Accessions,targetVersion = "v22") result2[c(341:345),] ## ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ library(miRBaseConverter) data(miRNATest) miRNANames = miRNATest$miRNA_Name result1 = miRNA_NameToAccession(miRNANames,version = "v18") result1[c(341:345),] ## ----message = TRUE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ library(miRBaseConverter) data(miRNATest) miRNANames = miRNATest$miRNA_Name result1 = miRNAVersionConvert(miRNANames,targetVersion = "v13",exact = TRUE) result1[c(341:345),] result2 = miRNAVersionConvert(miRNANames,targetVersion = "v20",exact = TRUE) result2[c(341:345),] ## ----message = TRUE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ library(miRBaseConverter) data(miRNATest) miRNANames = miRNATest$miRNA_Name #### Step 1. Check the possible version for miRNAs data(miRNATest) miRNANames = miRNATest$miRNA_Name version=checkMiRNAVersion(miRNANames, verbose = FALSE) #### Step 2. miRNA Names to miRBase Accessions with the specific version information result1 = miRNA_NameToAccession(miRNANames,version = version) #### Step 3. miRBase Accessions to miRNA Names of the target version result2 = miRNA_AccessionToName(result1[,2],targetVersion = "v22") result2[c(341:345),] ## ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ library(miRBaseConverter) data(miRNATest) miRNANames=miRNATest$miRNA_Name result1=miRNA_MatureToPrecursor(miRNANames) head(result1) ## ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ library(miRBaseConverter) miRNANames=c("pma-mir-100a","sko-mir-92a","hsa-mir-6131","mtr-MIR2655i", "mmu-mir-153","mtr-MIR2592am","mml-mir-1239","xtr-mir-128-2","oan-mir-100", "mmu-mir-378b","hsa-miR-508-5p","mmu-miR-434-3p") result2=miRNA_PrecursorToMature(miRNANames) head(result2) ## ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ library(miRBaseConverter) ## The input is miRNA Accessions Accessions=miRNATest$Accession Family_Info1=checkMiRNAFamily(Accessions) head(Family_Info1) ##The input is miRNA names miRNANames=miRNATest$miRNA_Name version=checkMiRNAVersion(miRNANames,verbose = FALSE) result=miRNA_NameToAccession(miRNANames,version=version) Accessions=result$Accession Family_Info2=checkMiRNAFamily(Accessions) head(Family_Info2) ## ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ library(miRBaseConverter) data(miRNATest) Accessions = miRNATest$Accession result1 = getMiRNASequence(Accessions,targetVersion = "v13") head(result1) result2 = getMiRNASequence(Accessions,targetVersion = "v22") head(result2) ## ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ library(miRBaseConverter) getAllVersionInfo() ## ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ library(miRBaseConverter) allSpecies=getAllSpecies() head(allSpecies) ## ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ library(miRBaseConverter) miRNAs=getAllMiRNAs(version="v22", type="all", species="hsa") head(miRNAs) ## ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ #### 1. The input is a miRNA Name name = "hsa-miR-26b-5p" result1 = miRNA_NameToAccession(name) Accession = result1$Accession result2 = getMiRNAHistory(Accession) result2 ## ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ #### 2. The input is miRNA Accession Id Accession = "MIMAT0000765" result3 = getMiRNAHistory(Accession) result3 ## ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ library(miRBaseConverter) miRNA_Tab=getMiRNATable(version="v22",species="hsa") head(miRNA_Tab) ## ----eval=FALSE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # library(miRBaseConverter) # Accessions=miRNATest$Accession[1:10] # goTo_miRBase(Accessions) ## ----eval=FALSE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # library(miRBaseConverter) # Accessions=miRNATest$Accession # Family_Info=checkMiRNAFamily(Accessions) # FamilyAccessions=Family_Info$FamilyAccession[1:15] # goTo_miRNAFamily(FamilyAccessions)