AD Enrichment Analysis

Last updated: 2024-10-15

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Knit directory: m6A_in_disease_genetics/

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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/AD_h2g_enrichment.Rmd) and HTML (docs/AD_h2g_enrichment.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
Rmd	31b6e55	Jing Gu	2024-10-15	make xlim ranges consistent
html	87ec047	Jing Gu	2024-10-14	Build site.
Rmd	af7cb31	Jing Gu	2024-10-14	tested enrichment for adult brain dataset
html	362f468	Jing Gu	2024-10-01	Build site.
Rmd	01e2114	Jing Gu	2024-10-01	m6A enrichment for AD risk variants

Estimating h2g enrichment with LDSC

GWAS: Bellenguez et al.(2022) harmonized summary statistics.

LDSC parameters:

GWAS variants filtered by Hapmap3 SNPs
LD computed based on Europeans from 1000 genome project
Baseline annotations from BaselineLD_v2.2
m6A annotations one at a time

Collecting m6A peaks

[1] "Fetal m6A peaks quantiles:"

        V1 X0. X25. X50.   X75. X100.
1    Brain  55  201  328    607  8466
2    Heart  53  158  248    439 18918
3   Kidney  57  182  285    498  7736
4    Liver  52  161  250    425  7639
5     Lung  64  177  271    453  6965
6   Muscle  57  192  305    523 15627
7 Placenta  55  171  265    461  7060
8  Stomach  67  195  300 504.25  4869
9   merged  54  184  290    514 18918

[1] "Adult m6A peaks quantiles:"

Enrichment results in barplots

Labels on top of the bars: enrichment p-values
Legend for y-axis: annotation (percent of genome-wide variants that fall in the annotation peaks)

[[1]]

Version	Author	Date
87ec047	Jing Gu	2024-10-14


[[2]]

Version	Author	Date
87ec047	Jing Gu	2024-10-14


[[3]]

Version	Author	Date
87ec047	Jing Gu	2024-10-14


[[4]]

Version	Author	Date
87ec047	Jing Gu	2024-10-14

R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.3.13-el7-x86_64/lib/libopenblas_haswellp-r0.3.13.so

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[10] LC_TELEPHONE=C       LC_MEASUREMENT=C     LC_IDENTIFICATION=C 

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
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[59] rlang_1.1.3                 grid_4.2.0                 
[61] RCurl_1.98-1.14             rstudioapi_0.15.0          
[63] rjson_0.2.21                htmlwidgets_1.6.4          
[65] crosstalk_1.2.1             labeling_0.4.3             
[67] bitops_1.0-7                rmarkdown_2.26             
[69] restfulr_0.0.15             gtable_0.3.5               
[71] codetools_0.2-19            R6_2.5.1                   
[73] GenomicAlignments_1.34.1    knitr_1.46                 
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[77] rprojroot_2.0.4             stringi_1.7.6              
[79] parallel_4.2.0              Rcpp_1.0.12                
[81] vctrs_0.6.5                 tidyselect_1.2.1           
[83] xfun_0.43

AD Enrichment Analysis

Jing Gu

2024-10-15

Estimating h2g enrichment with LDSC

Collecting m6A peaks

Enrichment results in barplots