asthma_prelim_results
Last updated: 2021-10-26
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Knit directory: funcFinemapping/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | db3c6f9 | Jing Gu | 2021-10-26 | test enrichment for asthma risk variants |
cell-type specific annotations
- Caldero et al. 2019 - ATAC-Seq data for FACS-sorted cells from whole blood I extracted ATAC-Seq peaks specific to each immune cell type from the count table that consists of a union set of peaks across cells based on the provided cutoffs.
Rheumatoid arthritis
This analysis was done to replicate the enrichment results from figure 5b in the paper. Overall, the magnitude of enrichment estimates are much smaller than that in figure 5b. It is possible that we did not use the same GWAS dataset. They used LDSC to estimate enrichment estimates. I will check how they ran LDSC over these annotations. The stimulated immune cells tend to have slightly higher enrichment estimates, but not as significant due to overlapped CIs. However, the figure in the paper demonstrates strong enrichment of stimulated-related peaks for cells such as Bulk B, naive B, CD8+ T and Th1. 
Adult-Onset Asthma
For Asthma, we did not see stronger enrichment of stimulated-related peaks compared with resting ones. But overall all immune cells whether or not stimulated (except for the stimulated mature NK) are significantly enriched for GWAS risk variants. 
Allergy
Joint Enrichment of a pair of annotations
Adult-Onset Asthma
A pair of annotations - stimulated and resting for each immune cell type was jointly tested for their enrichment of GWAS risk variants. We observed many cell types share GWAS association signals. Conditional on resting cells,there are five stimulated cell types still show enrichment including Naive B, Memory B, CD8+ T , Naive CD8+ T and Naive Tregs cells. 
Annotations - Differential accessible peaks
Caldero et al. 2019
- Significant differentially accessible regions when compared to progenitor cells
- Significant differentially accessible regions under stimulation
sessionInfo()R version 4.0.4 (2021-02-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)
Matrix products: default
BLAS/LAPACK: /software/openblas-0.3.13-el7-x86_64/lib/libopenblas_haswellp-r0.3.13.so
locale:
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[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] knitr_1.31 ggplot2_3.3.3 workflowr_1.6.2
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