This directory contains the R files used for the course of Statistics Applied to Bioinformatics.
source('http://www.bigre.ulb.ac.be/courses/statistics_bioinformatics/R-files/config.R')
Installation and configuration | |
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install_packages.R | Installation of some R packages used for the course |
config.R | Defines the configuration (directories, web site, ...), creates the directory to store the results of the practicals, and load the general utilities. This script should be sourced before other scripts. |
Descriptive statistics | |
central_tendency_dna_chip.R | Plot distribution of a DNA chip experiment |
central_tendency_yeast_orf_lengths.R | Plot distribution of yeast ORF lengths |
Theoretical distributions | |
geometric.R | Geometric distribution (figures) |
hypergeometric_series.R | Hypergeometric distribution (figures) |
hypergeometric_recursion.R | Recursive computation of the hypergeometric |
hypergeometric_versus_binomial.R | Comparison between hypergeometric and binomial (table + figure) |
binomial.R | Figure with the binomial density and distribution function |
binomial_series.R | Series of binomial distributions: effect of the probability of succcess at each trial (p) |
poisson_series.R | Series of Poisson distributions: effect of the mean |
binomial_to_normal.R | Series of binomial distributions with an increasing number of trials, to illustrate convergence towards the normal distribution |
student.R | Series of Student distributions with increasing degrees of freedom, to illustrate the convergence towards the normal distribution. |
Sampling and estimation | |
sampling_mean_distribution.R | Illustration of the effect of sample size on the variance of the mean estimate. |
Fitting | |
fitting_normal_examples.R | Histograms with the fitting of a normal curve on different data sets |
Hypothesis testing | |
conformity_tests.R | Illustrations of the conformity tests.
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student_test.R | Student test, multiple testing - select differentially expressed genes in a microarray data experiment (Golub 1999). |
Utilities | |
util/util.R | General utilities (export scripts) |
util/util_descr_stats.R | Descriptive statistics |
util/util_central_tendency.R | Plot a histogram with the indication of central tendency and dispersion parameters |
util/util_student_test_multi.R | Efficient implementation to apply the Student test (Welch version) to each row of an array. |
util/util_test_fitting_binomial.R | Test the fitting of a binomial distribution on a sample distribution. |
util/util_test_fitting_poisson.R | Test the fitting of a Poisson distribution on a sample distribution. |
util/util_test_fitting_normal.R | Test the fitting of a normal distribution on a sample distribution. |
util/util_chip_analysis.R | Plot gene expression profiles, K-mean clustering with profiles, SVD plot. |
Clustering | |
clustering_kmeans.R | Illustrations of mobile canters and K-means clustering |
clustering_carbon_sources.R | Illustration of clustering (hierarchiacl and K-means) with Gasch data (yeast growth with different carbon sources) |
Examples of microarray data analysis | |
spellman98/ | Directory with the R scripts fir the analysis of cell cycle data from Spellman 1998 |
load_spellman.R | load cell cycle data from Spellman 1998 |
spellman_analysis.R | K-means profiles and SVD with cell cycle data from Spellman 1998 |
Solutions to the exercises of the practicals | |
exercises/word_count_distrib.R | Fitting |
Solutions to the exercises from the book | |
exercises_probabilities.R | Probabilities |
Theoretical distributions | |
Hypothesis testing | |
Significance tests | |
Discriminant analysis |