bch441-work-abc-units/BIN-ALI-Similarity.R

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2017-09-12 20:09:20 +00:00
# BIN-ALI-Similarity.R
#
# Purpose: A Bioinformatics Course:
# R code accompanying the BIN-ALI-Similarity unit.
#
# Version: 0.1
#
# Date: 2017 08 28
# Author: Boris Steipe (boris.steipe@utoronto.ca)
#
# Versions:
# 0.1 First code copied from 2016 material.
#
# TODO:
#
#
# == DO NOT SIMPLY source() THIS FILE! =======================================
# If there are portions you don't understand, use R's help system, Google for an
# answer, or ask your instructor. Don't continue if you don't understand what's
# going on. That's not how it works ...
# ==============================================================================
# = 1 Mutation Data matrix
# First, we install and load the Biostrings package.
if (!require(Biostrings, quietly=TRUE)) {
source("https://bioconductor.org/biocLite.R")
biocLite("Biostrings")
library(Biostrings)
}
# Biostrings contains mutation matrices and other useful datasets
data(package = "Biostrings")
# Let's load BLOSUM62
data(BLOSUM62)
# ... and see what it contains. (You've seen this before, right?)
BLOSUM62
# We can simply access values via the row/column names to look at the data
# for the questions I asked in the Assignment on the Wiki:
BLOSUM62["H", "H"]
BLOSUM62["S", "S"]
BLOSUM62["L", "K"]
BLOSUM62["L", "I"]
BLOSUM62["R", "W"]
BLOSUM62["W", "R"] # the matrix is symmetric!
# = 1.1 <<<Subsection>>>
# = 1 Tasks
# [END]