Last updated: 2024-04-17
Checks: 2 0
Knit directory: pop_spec_eqtl_ml/
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| Rmd | f5d4894 | ibeasley | 2021-07-12 | Update index |
| Rmd | ac43b43 | ibeasley | 2021-07-12 | Start workflowr project. |
Overview:
This page and the analysis it documents is broken into two sections: paper, and full thesis. The paper section documents analysis completed specifically for the paper comparing definitions of portability. The full thesis section documents a broader set of analyses completed as part of Isobel’s masters thesis project (2021-2022).
Combining summary statistics across studies
The first step in our investigation is to combine eQTL summary statistics from multiple studies in the same tissue. Pages in this section contain information about investigations, decisions and final procedures used to combine single population eQTL summary statistics from relevant tissues together.
LD matrix estimation
Determining eQTL portability at the eSNP level
Command line scripts:
Command line scripts for labeling eQTLs as portable across a pair of populations/datasets in the same study group (i.e. Mogil, Mak or Natri) are all found in the code/call_pop_spec_shared folder. These scripts use the datasets found in output/combined_eqtl_summary_stats as input, produced in the above data haramonising analyses.
Analysis used to produce Figure 2 Upset Plots
Related summary statistics for Figure 2
Analysis used to produce Figure 3 Pairwise sharing plots
Analysis used to produce Figure 3 Power Associated Factor Correlations
Colocalisation Analysiss
Command line scripts:
Requires that additional previous analysis steps to make LD matrices from 10000 genomes and Indonesian vcf data have been run. Additionally these command line scripts also call functions from code/coloc/coloc_functions.R and code/utils/paper_plotting_functionsR.
mashr analysis
Impact of using mashr to account for power differences across studies
Supplementary analyses