Table 5.
Functions and descriptions of LncFinder R package
| Function | Description | Option |
|---|---|---|
| Functions for classic features extraction | ||
| compute_EIIP() | Compute EIIP-derived features | 1. spectrum.percent: set the percentage of the sorted power spectrum; 2. quantile.probs: set the quantile interval |
| compute_EucDist() | Compute Euclidean-distance features | 1. k: set the sliding window size;2. step: set the sliding window step; 3. on.ORF: calculate features on ORF region |
| compute_FickettScore() | Compute Fickett TESTCODE Score | on.ORF: calculate Fickett TESTCODE Score on ORF region |
| compute_GC() | Compute GC content | on.ORF: calculate GC content on ORF region |
| compute_hexamerScore() | Compute hexamer score | see compute_EucDist() |
| compute_kmer() | Compure k-mer features | improved.mode: use the improved method proposed by PLEK; other options see compute_EucDist() |
| compute_LogDist() | Compure Logarithm-distance | see compute_EucDist() |
| compute_pI() | Compure isoelectric point | 1. on.ORF: calculate isoelectric point on ORF region;2. ambiguous.base: take ambiguous bases into account |
| find_orfs() | Find ORFs | reverse.strand: find ORFs on the reverse strand |
| Functions for LncRNA identification and new classifier construction | ||
| lnc_finder() | Identify lncRNAs using LncFinder | 1. svm.model: select species, such as human, mouse and wheat; 2. SS.features: use multi-scale secondary structure features |
| build_model() | Build new model using LncFinder | see lnc_finder() |
| extract_features() | Extract features proposed by LncFinder | SS.features: extract multi-scale secondary structure features |
| read_SS() | Load external secondary structure information | |
| run_RNAfold() | Run RNAfold and capture the results | |
| svm_cv() | Perform cross validation for SVM model | 1. folds.num: set the number of folds for cross-validation;2. seed: set the seed for random number generation; other parameters for SVM model training |
| svm_tune() | Tune SVM model | see svm_cv() |
This table briefly summaries the main functions of LncFinder R package. All functions and descriptions are based on LncFinder R Package (version 1.1.2). The package will be updated regarlarly. Refer to Supplementary File 4 - R package Manual for detailed descriptions and examples.