20240310_mpra_analysis

This is the most up to date replication analysis of Mouri et al. and there are multiple other small projects in here as well.

The main folder architecture is that you take a results table from primary data (ex. OLJR.C_Tcell_emVAR_glm_20240310.out) and plug it into the 20240310_mpra_merge_creation.Rmd. This creates the MPRA merge table in hg19 which you then plug into 20240310_mpra_hg_19_to_38.Rmd. This generates a hg19, hg38 and a hg19&38 table. Then plug those tables into 20240310_mouri_et_al_replication_code_in_line.Rmd and generate the MPRA plots. These plots are stores in the plots_dir you specify in the code. There are currently four cell types for this analysis (primary tcell, unstimulated jurkat, stimulated jurkat and GM12878). Only primary tcells and unstimualted jurkats will go into the paper.

Side projects to find MPRA variant enrichment in fine mapping data:

1. eqtl_enrichment

2. PICS2

3. UK_biobank_finemapping_enrichment