Description Usage Arguments Value Examples

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.

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

`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" |

vector of numbers of neighbors

1 2 3 4 | ```
getNofNeighbors("APE")
getNofNeighbors(c("NEAREST", "EARNEST"))
getNofNeighbors("N")
getNofNeighbors("N", method="codon", libscheme="NNK")
``` |

peptider documentation built on May 29, 2017, 3:58 p.m.

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