Welcome to the polysel GITHUB repository. Here you can find code, examples, scripts and data sets to run a gene set enrichment test to detect pathways enriched with signals of polygenic selection.
We use the following folder structure:
- polysel
- R - R files with all functions needed to run the pipeline
- data - Input text files with gene and gene set information, but also the R data object files that are created during data preparation. Each project has its own subfolder
- empfdr - Output files from the creation of the p-value null distribution (see below)
- log - Location of error and output log files, mainly used on the cluster
- script - Script files to run the pipeline on a cluster
- results - Results of the gene set enrichment test, namely a list of gene sets with their scores and p and q values
When you are running the pipeline with your own data sets or one of the example sets, we advice to use the same structure, both on your PC and on a computer cluster.
In the root folder of this project, you will find examples explaining step by step how to run the enrichment pipeline. We strongly encourage you to try one or more of them before running the pipeline with your own data.
Primates project: Detection of pathways affected by positive selection in primate lineages ancestral to humans
-
example_primates_homininae.html; click here for a html preview
-
example_primates_hominidae.html; click here for a html preview
Human populations project: Evidence for Polygenic Adaptation to Pathogens in the Human Genome
- example_humanpops.html; click here for a html preview
Altitude project: Widespread Signals of Convergent Adaptation to High Altitude in Asia and America
- example_altitude.html; click here for a html preview
Daub, J.T. et al. (2016). Detection of pathways affected by positive selection in primate lineages ancestral to humans Mol Biol Evol 34, 1391–1402.
Daub, J.T. et al. (2013). Evidence for Polygenic Adaptation to Pathogens in the Human Genome Mol Biol Evol 30, 1544–1558.
Foll, M., Gaggiotti, O.E., Daub, J.T., Vatsiou, A., and Excoffier, L. (2014). Widespread Signals of Convergent Adaptation to High Altitude in Asia and America The American Journal of Human Genetics 95, 394–407.