Dry lab for exploring miRNA-mRNA relationships


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Documentation for package ‘miRLAB’ version 1.12.0

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miRLAB-package A dry lab for exploring miRNA-mRNA relationships
Borda Ensemble method for miRNA target prediction using Borda count election
BordaTopk Ensemble method for miRNA target prediction using Borda count election with topk targets
bRank Extract topk predicted targets of a miRNA Rank all the targets of a miRNA and extract the topk targets
convert Convert miRNA symbols from a miRBase version to another
Dcov miRNA target prediction with the Distance correlation method
DiffExpAnalysis Differentially expressed analysis
Elastic miRNA target prediction with the Elastic-net regression coefficient method
experiment Function for validate the results from all 12 methods.
Extopk Extract top k miRNA-mRNA interactions
filterAndCompare Filter and compare the validation results from 12 methods Keep the miRNAs that have at least noVal confirmed targets and compare the validation results from all methods.
getData getData from GDC
GOBPenrichment Functional enrichment analysis
Hoeffding miRNA target prediction with the Hoeffding correlation coefficient method
ICPPam50 Identify miRNA targets by ICP and PAM50
IDA miRNA target prediction with the IDA method
identifymiRTargetsByEnsemble Identify the top miRNA targets by an ensemble method with ICP-PAM50, Pearson and Lasso
identifymiRTargetsByICPPam50 Identify the top miRNA targets by ICP and PAM50
ImputeNormData Filter, impute, and normalise data.
KEGGenrichment Functional enrichment analysis KEGG enrichment analysis for a gene list
Kendall miRNA target prediction with the Kendall correlation coefficient method
Lasso miRNA target prediction with the Lasso method
MI miRNA target prediction with mutual information method
miRLAB A dry lab for exploring miRNA-mRNA relationships
Pearson miRNA target prediction with the Pearson correlation coefficient method
ProMISe miRNA target prediction with the ProMISe method
RDC miRNA target prediction with the Randomized Dependence Coefficient method
Read Read dataset from csv file
ReadExtResult Read results from other methods
readHeader Read the header of the dataset
Spearman miRNA target prediction with the Spearman correlation coefficient method
Standardise Stardarsise the dataset Stadardise the dataset to have mean=0 and std=1 in each column.
ValidateAll Validate the targets of all miRNA using both experimentally confirmed and transfection data
Validation Validate the targets of a miRNA
ValidationT Validate the targets of a miRNA using transfection data
Zscore miRNA target prediction with the Z-score method