peptider: Evaluation of Diversity in Nucleotide Libraries

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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 <erichare@iastate.edu>
License
GPL-3
Version
0.2.2
URLs

View on CRAN

Man pages

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

Files in this package

peptider
peptider/NAMESPACE
peptider/data
peptider/data/schemes.rda
peptider/data/BLOSUM80.rda
peptider/R
peptider/R/tabulate.r
peptider/R/peptider.r
peptider/README.md
peptider/MD5
peptider/DESCRIPTION
peptider/man
peptider/man/scheme.Rd
peptider/man/BLOSUM80.Rd
peptider/man/schemes.Rd
peptider/man/diversity.Rd
peptider/man/detect.Rd
peptider/man/codons.Rd
peptider/man/coverage.Rd
peptider/man/generateCustomLib.Rd
peptider/man/genNeighbors_reduced.Rd
peptider/man/encodingReduce.Rd
peptider/man/getNeighbors.Rd
peptider/man/generateCustom.Rd
peptider/man/generateCustomNei.Rd
peptider/man/libBuild.Rd
peptider/man/generateCustomProbs.Rd
peptider/man/libscheme.Rd
peptider/man/efficiency.Rd
peptider/man/genNeighbors.Rd
peptider/man/getChoices.Rd
peptider/man/makowski.Rd
peptider/man/getNofNeighbors.Rd
peptider/man/ppeptide.Rd
peptider/man/getCounts.Rd