Evaluation of Diversity in Nucleotide Libraries

Documentation for package ‘peptider’ version 0.2.2

BLOSUM80	BLOSUM80 matrix
codons	Compute the number of codon representations for a (vector of) peptide sequence(s)
coverage	Coverage as expected number of peptides given all possible peptides
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 information
generateCustomNei	For a given scheme, generate a dataset with the neighborhood information
generateCustomProbs	For a given scheme, generate a dataset with the peptide probabilities
genNeighbors	Calculate neighborhood distribution
genNeighbors_reduced	Calculate neighborhood distribution
getChoices	Get the number of peptides that reduce to a particular reduced encoding
getCounts	Get the counts possible for each scheme and k
getNeighbors	Find all neighbors of degree one for a set of peptide sequences
getNofNeighbors	Compute the number of neighbor of degree one for a set of peptide sequences
libBuild	Build peptide library of k-length sequences according to specified scheme
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