Repository for the project "An exploration of linkage fine-mapping on sequences from case-control studies" of Payman Nickchi, Charith (Bhagya) Karunarathna and Jinko Graham
Initially, for 500 populations, Payman and Bhagya (Charith) simulated:
- SNV sequences for the entire population using msprime and
- phenotypes under the ALTERNATIVE HYPOTHESIS OF ASSOCIATION for the entire population. They then randomly sampled 50 case individuals and 50 control (non-case) individuals from the population. The analyses for this initial phase are described in the document Workflow_Document.pdf.
Later, they took the population-level sequence datasets generated by msprime in the initial phase and re-simulated population-level phenotypes under the NULL HYPOTHESIS OF NO ASSOCIATION. Again, they randomly sampled 50 cases and 50 controls from the population. The analyses for this second "null" phase are NOT documented (except for here in this README), but pertain to the scripts: GetNullSample.R, GetNullSample_Utillity_Functions.R, null_ECDF.R and null_ECDF_Utillity_Functions.R in the repository.
Queries may be directed to Payman Nickchi at [email protected] or Bhagya (Charith) Karunarathna at [email protected].