Evaluation of diversity in peptide libraries, including NNN, NNB, NNK/S, and 20/20 schemes. Custom encoding schemes can also be defined. Metrics for evaluation include expected coverage, relative efficiency, and the functional diversity of the library. Peptide-level inclusion probabilities are computable for both the native and custom encoding schemes.
|Author||Heike Hofmann [aut], Eric Hare [aut, cre], GGobi Foundation [aut]|
|Date of publication||2015-09-16 10:05:27|
|Maintainer||Eric Hare <firstname.lastname@example.org>|
BLOSUM80: BLOSUM80 matrix
codons: Compute the number of codon representations for a (vector of)...
coverage: Coverage as expected number of peptides given all possible...
detect: Detection probability in a single library of size N
diversity: Diversity according to peptides paper (Sieber)
efficiency: Relative efficiency of a library
encodingReduce: Reduce the regular encoding to an easier/faster format
generateCustom: Generate peptide and library information for a given scheme
generateCustomLib: For a given scheme, generate a dataset with the library...
generateCustomNei: For a given scheme, generate a dataset with the neighborhood...
generateCustomProbs: For a given scheme, generate a dataset with the peptide...
genNeighbors: Calculate neighborhood distribution
genNeighbors_reduced: Calculate neighborhood distribution
getChoices: Get the number of peptides that reduce to a particular...
getCounts: Get the counts possible for each scheme and k
getNeighbors: Find all neighbors of degree one for a set of peptide...
getNofNeighbors: Compute the number of neighbor of degree one for a set of...
libBuild: Build peptide library of k-length sequences according to...
libscheme: Get the specified library scheme
makowski: Diversity index according to Makowski
ppeptide: Probability of detection of a peptide sequence
scheme: Get the specified library scheme definition
schemes: Built-in library schemes for peptider