New unit RPR-Biostrings.R

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# Purpose: A Bioinformatics Course:
# R code accompanying the RPR-Biostrings unit.
#
# Version: 0.1
# Version: 1.0
#
# Date: 2017 08 28
# Date: 2017 10 20
# Author: Boris Steipe (boris.steipe@utoronto.ca)
#
# Versions:
# 1.0 2017 Revisions
# 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 The Biostrings package
#TOC> ==========================================================================
#TOC>
#TOC> Section Title Line
#TOC> ---------------------------------------------------------
#TOC> 1 The Biostrings package 53
#TOC> 2 Getting Data into Biostrings Objects 82
#TOC> 3 Working with Biostrings Objects 102
#TOC> 3.1 Properties 105
#TOC> 3.2 Subsetting 142
#TOC> 3.3 Operators 154
#TOC> 3.4 Transformations 161
#TOC> 4 Getting Data out of Biostrings Objects 168
#TOC> 5 More 177
#TOC> 5.1 Views 179
#TOC> 5.2 Iranges 191
#TOC> 5.3 StringSets 197
#TOC>
#TOC> ==========================================================================
# This is a very brief introduction to the biostrings package, other units will
# be using more of the biostrings functions.
# = 1 The Biostrings package ==============================================
# First, we install and load the Biostrings package from bioconductor
# First, we install and load the Biostrings package.
if (!require(Biostrings, quietly=TRUE)) {
source("https://bioconductor.org/biocLite.R")
biocLite("Biostrings")
library(Biostrings)
}
# This is a large collection of tools ...
help(package = "Biostrings")
# At its core, Biostrings objects are "classes" of type XString (you can think
# of a "class" in R as a special kind of list), that can take on particular
# flavours for RNA, DNA or amino acid sequence information.
class(RNAString("AUG"))
class(DNAString("ATG"))
class(AAString("M"))
# An essential property of Biostrings objects is that they only allow letters
# from the applicable IUPAC alphabet:
RNAString("AUG")
DNAString("AUG") # Error! No "U" in IUPAC DNA codes
# = 2 Getting Data into Biostrings Objects ================================
# Example: read FASTA. Extract sequence. Convert to DNAString object.
x <- readLines("./data/S288C_YDL056W_MBP1_coding.fsa")
x <- dbSanitizeSequence(x)
myDNAseq <- DNAString(x) # takes the nucleotide sequence and conerts into a
# object of class DNAstring
# Multi FASTA files can be read directly ...
readDNAStringSet("./data/S288C_YDL056W_MBP1_coding.fsa") # Note: XStringSet
# ... and if you subset one sequence from the set, you get an XString object
( x <- readDNAStringSet("./data/S288C_YDL056W_MBP1_coding.fsa")[[1]] )
myDNAseq == x
identical(myDNAseq, x)
# = 1.1 <<<Subsection>>>
# = 3 Working with Biostrings Objects =====================================
# == 3.1 Properties ========================================================
str(myDNAseq)
length(nchar(x)) # This gives you the _number of nucleotides_!
# By comparison ...
length(x) # ... is 1: one string only. To get the number of
# characters in a string, you need nchar().
nchar(x) # However ...
nchar(myDNAseq) # ... also works.
# = 1 Tasks
uniqueLetters(myDNAseq)
# Count frequencies - with strings, you would strsplit() into a character
# vector and then use table(). biost
alphabetFrequency(myDNAseq)
# letterFrequency() works with a defined alphabet - such as what uniqueLetters()
# returns.
letterFrequency(myDNAseq, uniqueLetters(myDNAseq))
sum(letterFrequency(myDNAseq, c("G", "C"))) / length(myDNAseq) # GC contents
dinucleotideFrequency(myDNAseq)
barplot(sort(dinucleotideFrequency(myDNAseq)), cex.names = 0.5)
(x <- trinucleotideFrequency(myDNAseq))
barplot(sort(x), col="#4499EE33")
x[x == max(x)]
x[x == min(x)]
max(x) / min(x) # AAA is more than 13 times as frequent as CGT
# compare to a shuffled sequence:
(x <- trinucleotideFrequency(sample(myDNAseq)))
barplot(sort(x), col="#EEEE4433", add = TRUE)
# Interpret this plot.
# == 3.2 Subsetting ========================================================
# Subsetting any XString object works as expected:
myDNAseq[4:15]
# ... well - maybe not expected, because x[4:15] would not work.
# Alternatively to the "[" operator, use the subseq() function - especially for
# long sequences. This is far more efficient.
subseq(myDNAseq, start = 1, end = 30)
# == 3.3 Operators =========================================================
# RNAstring() and DNAstring() objects compare U and T as equals!
RNAString("AUGUCUAACCAAAUAUACUCAGCGAGAUAU") ==
DNAString("ATGTCTAACCAAATATACTCAGCGAGATAT")
# == 3.4 Transformations ===================================================
myDNAseq[4:15]
reverseComplement(myDNAseq[4:15])
translate(myDNAseq[4:15])
# = 4 Getting Data out of Biostrings Objects ==============================
# If you need a character object, use toString():
toString(myDNAseq[4:15])
# save() and load() works like on all other R objects.
# = 5 More ================================================================
# == 5.1 Views =============================================================
# Biostring "Views" are objects that store mutliple substrings of one
# Biostring object.
(myView <- Views(myDNAseq, start = c(1, 19, 37), end = c(15, 30, 45)))
# Views are convenient to store feature annotations
names(myView) <- c("Feature-A", "Feature-B", "Feature-C")
cat(sprintf("\n%s\t(%d)\t%s", names(myView), width(myView), myView ))
# == 5.2 Iranges ===========================================================
# Biostrings Iranges are like Views with a common start point. These can be
# useful for feature annotations. Instead of start/end you store start/width.
# == 5.3 StringSets ========================================================
# Biostring "StringSets" store multiple sequences.
#
ompA <- AAString("MKKTAIAIAVALAGFATVAQA")
sample(ompA) # sample can work directly on a Biostring object to shuffle it
x[1] <- toString(ompA)
for (i in 2:10) {
x[i] <- toString(sample(ompA))
}
shuffledPeptideSet <- AAStringSet(x)
names(shuffledPeptideSet) <- c("ompA", paste("shuffle.", 1:9, sep=""))
shuffledPeptideSet
length(shuffledPeptideSet)
width(shuffledPeptideSet)
alphabetFrequency(shuffledPeptideSet)
# [END]