kmeRs_similarity_matrix: Pairwise Similarity Matrix

In kmeRs: K-Mers Similarity Score Matrix

Description

The kmeRs_similarity_matrix function generates a pairwise similarity score matrix for for k length given k-mers vs. all possible k-mers combination. The pairwise similarity score is calculated using PAM or BLOSUM substitution matrix; 30, 40, 70, 120, 250 and 62, 45, 50, 62, 80, 100 matrix versions are available for PAM or BLOSUM, respectively. The results are evaluated by global similarity score; higher similarity score indicates more similar sequences for BLOSUM and opposite for PAM matrix.

Usage

kmeRs_similarity_matrix(kmers_given, compare_to = "",
  alignment_type = "global", k = 3, submat = "BLOSUM62",
  save_to_file = "")

Arguments

kmers_given	vector with given k-mers
compare_to	this parameter can have 3 different states, when: ” - the kmers_given will be compared to each other, default value; ALL - the kmers_given will be compared to all possible combinations given by k parameter e.g. N= 4^6 = 4096 combinations for 6-mers; 3rd option is to provide a list of k-mers which should be compared with the set given by the kmers_given parameter
alignment_type	type of alignment, default is 'global', could be 'local' or 'global', where 'global' represents Needleman-Wunsch global alignment; 'local' represents Smith-Waterman local alignment.
k	length of k-mers to calculate similarity matrix, higher values may slow down the computer, default value is k=3
submat	substitution matrix, default is 'BLOSUM62', but could be one of 'BLOSUM45', 'BLOSUM50', 'BLOSUM62', 'BLOSUM80', 'BLOSUM100', 'PAM30', 'PAM40', 'PAM70', 'PAM120', 'PAM250'
save_to_file	directory and file name; if value is declared the matrix will be saved to the given file name

Value

similarity matrix is returned as a data.frame

Examples

# Display BLOSUM matrix used for calculation

kmeRs_similarity_matrix(kmers_given = c("A", "T", "C", "G"), submat = "BLOSUM62")

kmeRs documentation built on May 2, 2019, 6:46 a.m.