find.similar.sequences: Find similar sequences.

In imminfo/tcr: Advanced Data Analysis of Immune Receptor Repertoires

Description

Return matrix M with two columns. For each element in row i and column j M[i,j] => distance between pattern(i) and data(j) sequences equal to or less than .max.errors. This function will uppercase .data and remove all strings, which have anything than A-Z letters.

Usage

find.similar.sequences(.data, .patterns = c(), .method = c('exact', 'hamm', 'lev'),
                       .max.errors = 1, .verbose = T, .clear = F)

exact.match(.data, .patterns = c(), .verbose = T)

hamming.match(.data, .patterns = c(), .max.errors = 1, .verbose = T)

levenshtein.match(.data, .patterns = c(), .max.errors = 1, .verbose = T)

Arguments

.data	Vector of strings.
.patterns	Character vector of sequences, which will be used for searching for neighbours.
.method	Which method use: 'exact' for exact matching, 'hamm' for Hamming Distance, 'lev' for Levenshtein distance.
.max.errors	Max Hamming or Levenshtein distance between strings. Doesn't use in 'exact' setting.
.verbose	Should function print progress or not. // DON'T USE IT
.clear	if T then remove all sequences with character "*" or "~".

Value

Matrix with two columns [i,j], dist(data(i), data(j)) <= .max.errors.

imminfo/tcr documentation built on June 13, 2020, 7:01 a.m.