Man pages for omarwagih/siftr
generate SIFT scores directly in R
| addLogs | Helper function for pseudo_diri, adds two logs |
| checkUnequalSequenceLengths | Check lengths of sequences are equal |
| diffAA | Generic information content function |
| diffAA.siftr_matrix | Number of unique amino acids per position |
| filterPredictions | Convert siftr matrix to data frame and filter out unreliable... |
| getEpsilonValues | Compute epsilon values |
| infoContent | Generic information content function |
| infoContent.siftr_matrix | Position information content |
| letterMatrix | Compute matrix of letters for the alignment |
| makePWM | Make PWM using pb weights and amino acid frequencies |
| makeSiftMatrix | Computes final matrix of sift scores returned to the user |
| medianInfoContent | Get median information content for each position |
| medianOfArray | SIFT version of median |
| normalizeWeights | Normalize pb weights matrix |
| pbWeights | Compute a weight for each amino acid at each position |
| pbWeightsNorm | Normalizes weights computed by pbWeights |
| percentIdentity | Compute percent identity between two sequences |
| positionInfoContent | Get median information content for a given position |
| predictFromAlignment | Predict sift scores from a protein alignment |
| print.siftr_matrix | Print siftr matrix |
| pseudo_diri | Get dirichelet pseudocounts for position i |
| removeIdenticalSeqs | Remove identical sequences in a list alignment |
| show.siftr_matrix | Print function for class siftr_matrix |
| summary.siftr_matrix | Summary for siftr matrix |
