Each of the sub-directories in the examples/ directory contains
a README giving an overview of the analysis, and a run.sh which
describes the set of commands used to run the analysis.
An example on Comprehensive Arrays for Relative Methylation, using a linear model with data from
Irizarry, R.A. et al. (2009). The human colon cancer methylome
shows similar hypo- and hypermethylation at conserved tissue-specific
CpG island shores. Nature Genetics, 41, 178-186.
The example is here: https://github.com/brentp/combined-pvalues/tree/master/examples/charm
An example comparing bisulfite sequencing data between Arabidopsis thaliana embryo and endosperm tissues using p-values from Fisher's exact test. The data is from:
Hsieh, T.F. et al. (2009). Genome-Wide Demethylation of Arabidopsis Endosperm.
Science, 324, 1451-1454.
The example is here: https://github.com/brentp/combined-pvalues/tree/master/examples/bs-seq
An example using t-test p-values from DamID technology followed by tiling arrays as reported in:
Kechris, K.J. et al. (2010)
Generalizing moving averages for tiling arrays using combined p-value
statistic. Statistical Applications in Genetics and Molecular Biology
9, Article 29.
The example is here: https://github.com/brentp/combined-pvalues/tree/master/examples/damid