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hyginn 2020-09-24 20:41:10 +10:00
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RPR-Biostrings.R
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@ -1,20 +1,15 @@
# tocID <- "RPR-Biostrings.R"
#
# ---------------------------------------------------------------------------- #
# PATIENCE ... #
# Do not yet work wih this code. Updates in progress. Thank you. #
# boris.steipe@utoronto.ca #
# ---------------------------------------------------------------------------- #
#
# Purpose: A Bioinformatics Course:
# R code accompanying the RPR-Biostrings unit.
#
# Version: 1.1
# Version: 1.2
#
# Date: 2017 10 - 2019 01
# Date: 2017-10 - 2020-09
# Author: Boris Steipe (boris.steipe@utoronto.ca)
#
# Versions:
# 1.2 2020 Updates
# 1.1 Change from require() to requireNamespace(),
# use <package>::<function>() idiom throughout,
# use Biocmanager:: not biocLite()
@ -35,33 +30,34 @@
#TOC> ==========================================================================
#TOC>
#TOC> Section Title Line
#TOC> ---------------------------------------------------------------
#TOC> 1 The Biostrings Package 55
#TOC> 2 Getting Data into Biostrings Objects 86
#TOC> 3 Working with Biostrings Objects 108
#TOC> 3.1 Properties 125
#TOC> 3.2 Subsetting 163
#TOC> 3.3 Operators 175
#TOC> 3.4 Transformations 182
#TOC> 4 Getting Data out of Biostrings Objects 189
#TOC> 5 More 198
#TOC> 5.1 Views 200
#TOC> 5.2 Iranges 214
#TOC> 5.3 StringSets 220
#TOC>
#TOC>
#TOC> Section Title Line
#TOC> -----------------------------------------------------------------
#TOC> 1 The Biostrings:: Package 56
#TOC> 2 Getting Data into Biostrings:: Objects 88
#TOC> 3 Working with Biostrings:: Objects 110
#TOC> 3.1 Properties 127
#TOC> 3.2 Subsetting 168
#TOC> 3.3 Operators 180
#TOC> 3.4 Transformations 187
#TOC> 4 Getting Data out of Biostrings:: Objects 194
#TOC> 5 More 203
#TOC> 5.1 Views 205
#TOC> 5.2 Iranges 219
#TOC> 5.3 StringSets 225
#TOC>
#TOC> ==========================================================================
# This is a very brief introduction to the biostrings package, other units will
# be using more of the biostrings functions.
# This is a very brief introduction to the Biostrings:: package, other units will
# be using more of the Biostrings:: functions.
# = 1 The Biostrings Package ==============================================
# = 1 The Biostrings:: Package ============================================
# First, we install and load the Biostrings package from bioconductor
# First, we install and load the Biostrings:: package from bioconductor (if we
# haven't done so already).
if (! requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
@ -75,7 +71,7 @@ browseVignettes("Biostrings") # available vignettes
data(package = "Biostrings") # available datasets
# At its core, Biostrings objects are "classes" of type XString (you can think
# 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.
@ -83,13 +79,13 @@ class(Biostrings::RNAString("AUG"))
class(Biostrings::DNAString("ATG"))
class(Biostrings::AAString("M"))
# An essential property of Biostrings objects is that they only allow letters
# An essential property of Biostrings:: objects is that they only allow letters
# from the applicable IUPAC alphabet:
Biostrings::RNAString("AUG")
Biostrings::DNAString("AUG") # Error! No "U" in IUPAC DNA codes
# = 2 Getting Data into Biostrings Objects ================================
# = 2 Getting Data into Biostrings:: Objects ==============================
# Example: read FASTA. Extract sequence. Convert to DNAString object.
@ -111,9 +107,9 @@ identical(biosDNAseq, Xseq) # ... and indeed the objects are deemed identical.
# = 3 Working with Biostrings Objects =====================================
# = 3 Working with Biostrings:: Objects ===================================
# Biostrings is a highly engineered package that is tightly integrated into
# Biostrings:: is a highly engineered package that is tightly integrated into
# the Bioconductor world - unfortunately that brings with it a somewhat
# undesirable level of computational overhead and dependencies. Using the
# package as we normally do - i.e. calling required functions with their
@ -162,8 +158,11 @@ max(triNuc) / min(triNuc) # AAA is more than 13 times as frequent as CGT
# compare to a shuffled sequence:
(triNuc <- Biostrings::trinucleotideFrequency(sample(biosDNAseq)))
barplot(sort(triNuc), col="#EEEE4433", add = TRUE)
max(triNuc)
# Interpret this plot.
(triNuc <- Biostrings::trinucleotideFrequency(sample(biosDNAseq)))
barplot(sort(triNuc), col="#EEEE4433")
max(triNuc)
# == 3.2 Subsetting ========================================================
@ -192,7 +191,7 @@ Biostrings::reverseComplement(biosDNAseq[4:15])
Biostrings::translate(biosDNAseq[4:15])
# = 4 Getting Data out of Biostrings Objects ==============================
# = 4 Getting Data out of Biostrings:: Objects ============================
# If you need a character object, use toString():
@ -219,7 +218,7 @@ 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
# 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.