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