AD Enrichment Analysis
Jing Gu
2024-10-14
Last updated: 2024-10-14
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Knit directory: m6A_in_disease_genetics/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| 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
[1] "base"
[2] "Coding_UCSC"
[3] "Conserved_LindbladToh"
[4] "CTCF_Hoffman"
[5] "DGF_ENCODE"
[6] "DHS_peaks_Trynka"
[7] "DHS_Trynka"
[8] "Enhancer_Andersson"
[9] "Enhancer_Hoffman"
[10] "FetalDHS_Trynka"
[11] "H3K27ac_Hnisz"
[12] "H3K27ac_PGC2"
[13] "H3K4me1_peaks_Trynka"
[14] "H3K4me1_Trynka"
[15] "H3K4me3_peaks_Trynka"
[16] "H3K4me3_Trynka"
[17] "H3K9ac_peaks_Trynka"
[18] "H3K9ac_Trynka"
[19] "Intron_UCSC"
[20] "PromoterFlanking_Hoffman"
[21] "Promoter_UCSC"
[22] "Repressed_Hoffman"
[23] "SuperEnhancer_Hnisz"
[24] "TFBS_ENCODE"
[25] "Transcr_Hoffman"
[26] "TSS_Hoffman"
[27] "UTR_3_UCSC"
[28] "UTR_5_UCSC"
[29] "WeakEnhancer_Hoffman"
[30] "GERP.NS"
[31] "GERP.RSsup4"
[32] "MAFbin1"
[33] "MAFbin2"
[34] "MAFbin3"
[35] "MAFbin4"
[36] "MAFbin5"
[37] "MAFbin6"
[38] "MAFbin7"
[39] "MAFbin8"
[40] "MAFbin9"
[41] "MAFbin10"
[42] "MAF_Adj_Predicted_Allele_Age"
[43] "MAF_Adj_LLD_AFR"
[44] "Recomb_Rate_10kb"
[45] "Nucleotide_Diversity_10kb"
[46] "Backgrd_Selection_Stat"
[47] "CpG_Content_50kb"
[48] "MAF_Adj_ASMC"
[49] "GTEx_eQTL_MaxCPP"
[50] "BLUEPRINT_H3K27acQTL_MaxCPP"
[51] "BLUEPRINT_H3K4me1QTL_MaxCPP"
[52] "BLUEPRINT_DNA_methylation_MaxCPP"
[53] "synonymous"
[54] "non_synonymous"
[55] "Conserved_Vertebrate_phastCons46way"
[56] "Conserved_Mammal_phastCons46way"
[57] "Conserved_Primate_phastCons46way"
[58] "BivFlnk"
[59] "Human_Promoter_Villar"
[60] "Human_Enhancer_Villar"
[61] "Ancient_Sequence_Age_Human_Promoter"
[62] "Ancient_Sequence_Age_Human_Enhancer"
[63] "Human_Enhancer_Villar_Species_Enhancer_Count"
[64] "Human_Promoter_Villar_ExAC"
[65] "m6A_hNPCL2_1" 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]]
[[2]]
[[3]]
[[4]]
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
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=C
[4] LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=C
[7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C
[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:
[1] ggplot2_3.4.0 rtracklayer_1.58.0 GenomicRanges_1.50.2
[4] GenomeInfoDb_1.34.9 IRanges_2.32.0 S4Vectors_0.36.2
[7] BiocGenerics_0.44.0 dplyr_1.1.4 data.table_1.15.4
[10] workflowr_1.7.1
loaded via a namespace (and not attached):
[1] MatrixGenerics_1.10.0 Biobase_2.58.0
[3] httr_1.4.7 sass_0.4.9
[5] jsonlite_1.8.8 R.utils_2.12.3
[7] bslib_0.7.0 getPass_0.2-2
[9] highr_0.10 GenomeInfoDbData_1.2.9
[11] Rsamtools_2.14.0 yaml_2.3.8
[13] pillar_1.9.0 lattice_0.22-5
[15] glue_1.7.0 digest_0.6.35
[17] promises_1.3.0 XVector_0.38.0
[19] colorspace_2.1-0 R.oo_1.26.0
[21] htmltools_0.5.8.1 httpuv_1.6.14
[23] Matrix_1.6-5 XML_3.99-0.16.1
[25] pkgconfig_2.0.3 zlibbioc_1.44.0
[27] scales_1.3.0 processx_3.8.3
[29] whisker_0.4.1 later_1.3.2
[31] BiocParallel_1.32.6 git2r_0.33.0
[33] tibble_3.2.1 farver_2.1.1
[35] generics_0.1.3 DT_0.33
[37] cachem_1.0.8 withr_3.0.0
[39] SummarizedExperiment_1.28.0 cli_3.6.2
[41] magrittr_2.0.3 crayon_1.5.2
[43] evaluate_0.23 ps_1.7.6
[45] R.methodsS3_1.8.2 fs_1.6.4
[47] fansi_1.0.6 tools_4.2.0
[49] BiocIO_1.8.0 lifecycle_1.0.4
[51] matrixStats_1.2.0 stringr_1.5.1
[53] munsell_0.5.1 DelayedArray_0.24.0
[55] callr_3.7.3 Biostrings_2.66.0
[57] compiler_4.2.0 jquerylib_0.1.4
[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
[75] fastmap_1.1.1 utf8_1.2.4
[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