Workshops/Saskatoon 2015-Exploratory Data Analysis

Introduction to Exploratory Data Analysis with R

 

Schedule

Please note: this schedule is a rough guideline only, we will be very flexible to adapt to class needs as we proceed.

Time	Thursday's Activities	Friday
09:00 – 10:30	Lecture and practicals: EDA	Lecture and practicals: Dimension reduction
10:30 – 11:00	Coffee break
11:00 – 12:30	Lecture and practicals: EDA	Lecture and practicals: Clustering
12:30 – 13:30	Lunch break
13:30 – 15:00	Lecture and practicals: Software development	Lecture and practicals:Clustering
15:00 – 15:30	Coffee break
13:30 – 15:00	Lecture and practicals: Regression	Lecture and practicals: Hypothesis testing

 

General Resources

• A concise reference card of R functions for data mining (pdf)

EDA

Slides

• EDA.pdf (pdf of slides)

Scripts

• EDA.R (the main script for this session)
•     SubsettingQuizAnswers.R(Answers, in case you don't already wrote them in your script)
• PlottingReference.R

Data

• GvHD.txt

Resources

 

Software

Links

• Regular_Expressions
• Software_Development
• R_knitr

Resources

• Using Projects with R Studio
• Software Carpentry
  • Best Practices for Scientific Computing, Wilson et al., PLoS Biology, Jan. 2014
• Version control in R Studio

 

Regression

Slides

• EDA_Regression.pdf (pdf of slides)

Scripts

• EDA_Regression.R (the main script for this session)

 

Dimension Reduction

Slides

Scripts

Resources

 

Clustering

Slides

Scripts

Resources

 

Hypothesis Testing

Slides

Scripts

Resources

 

Generally useful links

Help and Information

• The R help mailing list: https://stat.ethz.ch/mailman/listinfo/r-help
• Rseek: the specialized search engine for R topics: http://rseek.org/
• R questions on stackoverflow: http://stackoverflow.com/questions/tagged/r
• The Comprehensive R Archive Network CRAN: http://cran.r-project.org/
• The CRAN task-view collection: http://cran.r-project.org/web/views/
• Bioconductor task views: http://www.bioconductor.org/packages/release/BiocViews.html

Resources

• Weissgerber_(2015)_BeyondBarcharts.pdf

 

Notes