peptider (version 0.2.2)

getNeighbors: Find all neighbors 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.

Usage

getNeighbors(x, blosum = 1)

Arguments

x

(vector) of character strings of peptide sequences.

blosum

minimal BLOSUM loading, defaults to 1 for positive loadings only

Value

list of neighbor sequences

Examples

getNeighbors("APE")
getNeighbors(c("HI", "APE"))
getNeighbors(c("HI", "EARNEST", "APE"), blosum=3)
## degree 2 neighbors:
unique(unlist(getNeighbors(getNeighbors("APE"))))