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Course Outline
I. Introduction and preliminaries
1. Overview
- Enhancing R's usability: R and available GUIs
- RStudio
- Complementary software and documentation
- R and statistics
- Interactive use of R
- An introductory session
- Accessing help for functions and features
- R commands, case sensitivity, and other conventions
- Recalling and correcting previous commands
- Executing commands from or directing output to files
- Data persistence and object management
- Best practices in programming: Writing self-contained, readable code, including structured scripts, documentation, and markdown
- Installing packages via CRAN and Bioconductor
2. Reading data
- Text files (read.delim)
- CSV files
3. Basic manipulations; numbers, vectors, and arrays
- Vectors and assignment
- Vector arithmetic
- Generating regular sequences
- Logical vectors
- Handling missing values
- Character vectors
- Index vectors: selecting and modifying subsets of a dataset
- Arrays
- Array indexing and accessing subsections
- Index matrices
- The array() function and basic array operations (e.g., multiplication, transposition)
- Other object types
4. Lists and data frames
- Lists
- Constructing and modifying lists
- Concatenating lists
- Data frames
- Creating data frames
- Working with data frames
- Attaching arbitrary lists
- Managing the search path
5. Data manipulation
- Selecting and subsetting observations and variables
- Filtering and grouping
- Recoding and transformations
- Aggregation and combining datasets
- Creating partitioned matrices, using cbind() and rbind()
- Concatenation with arrays
- Character manipulation using the stringr package
- Introduction to grep and regexpr
6. Advanced data reading
- XLS and XLSX files
- readr and readxl packages
- SPSS, SAS, Stata, and other data formats
- Exporting data to txt, csv, and other formats
6. Grouping, loops, and conditional execution
- Grouped expressions
- Control statements
- Conditional execution: if statements
- Repetitive execution: for loops, repeat, and while
- Introduction to apply, lapply, sapply, and tapply
7. Functions
- Creating functions
- Optional arguments and default values
- Functions with a variable number of arguments
- Scope and its implications
8. Basic graphics in R
- Creating graphs
- Density plots
- Dot plots
- Bar plots
- Line charts
- Pie charts
- Boxplots
- Scatter plots
- Combining plots
II. Statistical analysis in R
1. Probability distributions
- R as a repository of statistical tables
- Examining the distribution of a dataset
2. Hypothesis testing
- Tests concerning a population mean
- Likelihood Ratio Test
- One-sample and two-sample tests
- Chi-Square Goodness-of-Fit Test
- Kolmogorov-Smirnov One-Sample Statistic
- Wilcoxon Signed-Rank Test
- Two-Sample Test
- Wilcoxon Rank Sum Test
- Mann-Whitney Test
- Kolmogorov-Smirnov Test
3. Multiple hypothesis testing
- Type I Error and False Discovery Rate (FDR)
- ROC curves and AUC
- Multiple Testing Procedures (Benjamini-Hochberg, Bonferroni, etc.)
4. Linear regression models
- Generic functions for extracting model information
- Updating fitted models
- Generalized linear models
- Families
- The glm() function
- Classification
- Logistic Regression
- Linear Discriminant Analysis
- Unsupervised learning
- Principal Components Analysis
- Clustering Methods (k-means, hierarchical clustering, k-medoids)
5. Survival analysis (survival package)
- Survival objects in R
- Kaplan-Meier estimate, log-rank test, parametric regression
- Confidence bands
- Analysis of censored (interval-censored) data
- Cox PH models with constant covariates
- Cox PH models with time-dependent covariates
- Simulation: Model comparison (comparing regression models)
6. Analysis of Variance
- One-Way ANOVA
- Two-Way Classification of ANOVA
- MANOVA
III. Worked problems in bioinformatics
- Short introduction to the limma package
- Microarray data analysis workflow
- Data download from GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1397
- Data processing (Quality Control, normalization, differential expression)
- Volcano plots
- Clustering examples and heatmaps
28 Hours
Testimonials (2)
knowledge of the trainer, tailor based, all topics covered
eleni - EUAA
Course - Forecasting with R
The real life applications using Statcan and CER as examples.
