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

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

1
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

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.