A Comprehensive Workflow for Long Non-coding RNA Identification
and Functional Analysis
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Documentation for package ‘lncRna’ version 0.99.3
Help Pages
| aggregateCodPot | Aggregate Coding Potential Tool Results |
| annotateInteractions | Annotate Genomic Interactions with Functional Enrichment Results |
| bestTool | Evaluate Performance of Coding Potential Tools |
| bestToolAtleast | Evaluate Performance of Agreement Thresholds |
| bestToolCombination | Evaluate Performance of Tool Combinations |
| calculateCM | Calculate and Filter Confusion Matrices for Tool Combinations |
| createTrainTestSets | Split a Set of Sequence Names into Training and Test Sets |
| evaluateToolCombinations | Evaluate Performance of Tool Combinations |
| evaluateToolsThresholds | Evaluate Agreement Thresholds Among Coding Potential Tools |
| findCisInteractions | Find Potential cis-Regulatory Interactions from FEELnc Output |
| findTransInteractions | Estimates trans-interactions between lncRNAs and target RNAs based on expression correlation. This function requires the 'Hmisc' and 'tidyr' packages. |
| getBiotypes | Extract Gene or Transcript Biotypes from a GRanges Object |
| getGtfStats | Extract Transcript Statistics from a GTF object |
| plotClockMetrics | Create Clock Plots for Confusion Matrix Metrics |
| plotRadarMetrics | Create Radar Plots for Confusion Matrix Metrics |
| plotSankeyInteractions | Plot Functional Interactions as a Sankey Diagram |
| plotVennCodPot | Create Venn Diagram from Coding Potential Results |
| prepareEvaluationSets | Prepare Data Sets for Performance Evaluation |