RPR-Biostrings

The biostrings R Package

 

Keywords:  Introduction to the biostrings bioconductor package

 

 

Caution!

This unit is under development. There is some contents here but it is incomplete and/or may change significantly: links may lead to nowhere, the contents is likely going to be rearranged, and objectives, deliverables etc. may be incomplete or missing. Do not work with this material until it is updated to "live" status.

 

Abstract

The biostrings package in the bioconductor project provides basic support for working with biological sequences. This unit introduces XString objects and some of their methods, and ways to get data into, and out of such objects.

 

This unit ...

Prerequisites

You need to complete the following units before beginning this one:

• RPR-FASTA (FASTA files with R)

 

Objectives

This unit will ...

• ... introduce the Biostrings package;
• ... teach how to get data into and out of XString, and how to perform simple analyses and transformations.

 

Outcomes

After working through this unit you ...

• ... can create DNAString, RNAString and AAString objects;
• ... can write code to analyze and transform them;
• ... are familiar with XStringSets, and Views and IRanges objects.

 

Deliverables

• Time management: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.
• Journal: Document your progress in your Course Journal. Some tasks may ask you to include specific items in your journal. Don't overlook these.
• Insights: If you find something particularly noteworthy about this unit, make a note in your insights! page.

 

Evaluation

Evaluation: NA

This unit is not evaluated for course marks.

 

Contents

Task:

 

• Open RStudio and load the ABC-units R project. If you have loaded it before, choose File → Recent projects → ABC-Units. If you have not loaded it before, follow the instructions in the RPR-Introduction unit.
• Choose Tools → Version Control → Pull Branches to fetch the most recent version of the project from its GitHub repository with all changes and bug fixes included.
• Type init() if requested.
• Open the file RPR-Biostrings.R and follow the instructions.

 

Note: take care that you understand all of the code in the script. Evaluation in this course is cumulative and you may be asked to explain any part of code.

 

 

Further reading, links and resources

• Biostrings Quick Overview ( summary of Biostrings functions (PDF))

 

Notes

 

Self-evaluation

 

 

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If in doubt, ask! If anything about this learning unit is not clear to you, do not proceed blindly but ask for clarification. Post your question on the course mailing list: others are likely to have similar problems. Or send an email to your instructor.

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About ...
 
Author:

Boris Steipe <boris.steipe@utoronto.ca>

Created:

2017-08-05

Modified:

2017-08-05

Version:

1.0

Version history:

• 1.0 First live version 2017
• 0.1 First stub

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