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peptider

R package for working with peptide libraries

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Install

install.packages('peptider')

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121

Version

0.2.2

License

GPL-3

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Maintainer

Eric Hare

Last Published

September 16th, 2015

Functions in peptider (0.2.2)

genNeighbors_reduced

Calculate neighborhood distribution
generateCustom

Generate peptide and library information for a given scheme
libscheme

Get the specified library scheme
detect

Detection probability in a single library of size N
generateCustomProbs

For a given scheme, generate a dataset with the peptide probabilities
coverage

Coverage as expected number of peptides given all possible peptides
makowski

Diversity index according to Makowski
ppeptide

Probability of detection of a peptide sequence
getChoices

Get the number of peptides that reduce to a particular reduced encoding
codons

Compute the number of codon representations for a (vector of) peptide sequence(s)
generateCustomNei

For a given scheme, generate a dataset with the neighborhood information
BLOSUM80

BLOSUM80 matrix
libBuild

Build peptide library of k-length sequences according to specified scheme
diversity

Diversity according to peptides paper (Sieber)
encodingReduce

Reduce the regular encoding to an easier/faster format
genNeighbors

Calculate neighborhood distribution
getCounts

Get the counts possible for each scheme and k
generateCustomLib

For a given scheme, generate a dataset with the library information
getNeighbors

Find all neighbors of degree one for a set of peptide sequences
schemes

Built-in library schemes for peptider
scheme

Get the specified library scheme definition
getNofNeighbors

Compute the number of neighbor of degree one for a set of peptide sequences
efficiency

Relative efficiency of a library