getNofNeighbors: Compute the number of neighbor of degree one for a set of...

In peptider: Evaluation of Diversity in Nucleotide Libraries

Description

first degree neighbors - a neighbor of a peptide is defined as a peptide sequence that differs in at most one amino acid from a given sequence. Additionally, we can restrict neighbors to regard only those sequences that have a certain minimal BLOSUM loading. Use this function for only a few peptide sequences. Any larger number of peptide sequences will take too much main memory.

Usage

getNofNeighbors(x, blosum = 1, method = "peptide", libscheme = NULL)

Arguments

x	(vector) of character strings of peptide sequences.
blosum	minimal BLOSUM loading, defaults to 1 for positive loadings only
method	character string, one of "peptide" or "codon". This specifies the level at which the neighbors are calculated.
libscheme	library scheme under which neighbors are being calculated. this is only of importance, if method="dna"

Value

vector of numbers of neighbors

Examples

getNofNeighbors("APE")
getNofNeighbors(c("NEAREST", "EARNEST"))
getNofNeighbors("N")
getNofNeighbors("N", method="codon", libscheme="NNK")

peptider documentation built on May 2, 2019, 2:43 a.m.