# 菜鸟的孟德尔随机化分析
孟德尔随机化（Mendelian Randomization, MR）的基本原理是：
以 GWAS 的结果为基础，引入随机分配的遗传变异（即 SNPs）作为随机化工具（工具变量 (instrumental variable, IV)），替代暴露因素。
- 一方面，实验对象、顺序和样本的分配被随机化，随机引起的误差、处理效应和样本偏倚得以消除；
- 另一方面，使用工具变量而不是暴露因素，规避了混杂因素和反向因果的影响，大大降低结果受未知因素影响的可能性。
于是，在 MR 中引入工具变量，有助于揭示暴露因素与结局的因果关系，保证了结论的可靠性。
项目文件说明
README.md：本文件，项目说明文档#_env_init.R：加载项目依赖#_subsetting：从数据集中提取子集，用于调试项目0_0folder_init.R：初始化每个孟德尔随机化分析的文件夹0_1data_formating.R：使用MungeSumstats::format_sumstats()格式化 GWAS 数据，以便后续分析1_correlation_analysis.R：基于关联性筛选 SNPs2_linkage_disequilibrium_analysis.R：基于连锁不平衡筛选 SNPs3_remove_weak_IV.R：基于 F 统计量筛选 SNPs4_remove_confounder.R：去可能引起混杂的 SNPs5_do_MR1.R：执行孟德尔随机化（Mendelian Randomization）分析5_do_MR2.R：绘制孟德尔随机化结果图
相关链接
开源协议
本项目采用 GNU 协议，详情请参阅 LICENSE。
常见问题及可能的解决方案
获取 FastTraitR 和 FastDownloader 包
用于去除混杂因素的 FastTraitR 和 FastDownloader 包由医工科研
提供，详情参见：FastDownloader 安装教程
。
PLINK 二进制程序安装
plinkbinr 包已包含了适用于各个 OS 的 PLINK 二进制程序，于是项目一般不再需要额外下载 PLINK 程序。
但若要特殊指定 PLINK 程序的位置，可以前往 PLINK 1.9 home 获取。
Session 信息
```
R version 4.3.3 (2024-02-29 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8 x64 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936
[2] LC_CTYPE=Chinese (Simplified)_China.936
[3] LC_MONETARY=Chinese (Simplified)_China.936
[4] LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.936
time zone: Asia/Shanghai
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets
[7] methods base
other attached packages:
[1] GenomicFiles_1.38.0
[2] BiocParallel_1.36.0
[3] MungeSumstats_1.10.1
[4] lubridate_1.9.3
[5] forcats_1.0.0
[6] stringr_1.5.1
[7] purrr_1.0.2
[8] readr_2.1.5
[9] tibble_3.2.1
[10] tidyverse_2.0.0
[11] SNPlocs.Hsapiens.dbSNP155.GRCh38_0.99.24
[12] SNPlocs.Hsapiens.dbSNP155.GRCh37_0.99.24
[13] BSgenome_1.70.2
[14] rtracklayer_1.62.0
[15] BiocIO_1.12.0
[16] MRPRESSO_1.0
[17] FastTraitR_1.0.0
[18] FastDownloader_1.0.0
[19] plinkbinr_0.0.0.9000
[20] friendly2MR_0.2.0
[21] cowplot_1.1.3
[22] ggfunnel_0.1.0
[23] ggforestplot_0.1.0
[24] ggplot2_3.5.0
[25] LDlinkR_1.4.0
[26] MendelianRandomization_0.9.0
[27] TwoSampleMR_0.5.11
[28] CMplot_4.5.1
[29] tidyr_1.3.1
[30] dplyr_1.1.4
[31] gwasglue_0.0.0.9000
[32] ieugwasr_0.2.2-9000
[33] gwasvcf_0.1.2
[34] VariantAnnotation_1.48.1
[35] Rsamtools_2.18.0
[36] Biostrings_2.70.3
[37] XVector_0.42.0
[38] SummarizedExperiment_1.32.0
[39] Biobase_2.62.0
[40] GenomicRanges_1.54.1
[41] GenomeInfoDb_1.38.8
[42] IRanges_2.36.0
[43] S4Vectors_0.40.2
[44] MatrixGenerics_1.14.0
[45] matrixStats_1.2.0
[46] BiocGenerics_0.48.1
loaded via a namespace (and not attached):
[1] splines_4.3.3 later_1.3.2
[3] bitops_1.0-7 filelock_1.0.3
[5] R.oo_1.26.0 XML_3.99-0.16.1
[7] lifecycle_1.0.4 lattice_0.22-6
[9] MASS_7.3-60.0.1 backports_1.4.1
[11] magrittr_2.0.3 openxlsx_4.2.5.2
[13] plotly_4.10.4 rmarkdown_2.26
[15] yaml_2.3.8 remotes_2.5.0
[17] httpuv_1.6.15 zip_2.3.1
[19] sessioninfo_1.2.2 pkgbuild_1.4.4
[21] DBI_1.2.2 abind_1.4-5
[23] pkgload_1.3.4 zlibbioc_1.48.2
[25] R.utils_2.12.3 RCurl_1.98-1.14
[27] rappdirs_0.3.3 GenomeInfoDbData_1.2.11
[29] MatrixModels_0.5-3 codetools_0.2-20
[31] DelayedArray_0.28.0 xml2_1.3.6
[33] tidyselect_1.2.1 shape_1.4.6.1
[35] gmp_0.7-4 BiocFileCache_2.10.2
[37] GenomicAlignments_1.38.2 jsonlite_1.8.8
[39] ellipsis_0.3.2 survival_3.5-8
[41] iterators_1.0.14 foreach_1.5.2
[43] tools_4.3.3 progress_1.2.3
[45] Rcpp_1.0.12 glue_1.7.0
[47] SparseArray_1.2.4 xfun_0.43
[49] usethis_2.2.3 withr_3.0.0
[51] numDeriv_2016.8-1.1 BiocManager_1.30.22
[53] fastmap_1.1.1 fansi_1.0.6
[55] SparseM_1.81 digest_0.6.35
[57] timechange_0.3.0 R6_2.5.1
[59] mime_0.12 colorspace_2.1-0
[61] arrangements_1.1.9 biomaRt_2.58.2
[63] RSQLite_2.3.6 R.methodsS3_1.8.2
[65] utf8_1.2.4 generics_0.1.3
[67] data.table_1.15.4 robustbase_0.99-2
[69] prettyunits_1.2.0 httr_1.4.7
[71] htmlwidgets_1.6.4 S4Arrays_1.2.1
[73] pkgconfig_2.0.3 gtable_0.3.4
[75] blob_1.2.4 htmltools_0.5.8.1
[77] profvis_0.3.8 scales_1.3.0
[79] png_0.1-8 knitr_1.46
[81] tzdb_0.4.0 rjson_0.2.21
[83] curl_5.2.1 cachem_1.0.8
[85] parallel_4.3.3 miniUI_0.1.1.1
[87] AnnotationDbi_1.64.1 restfulr_0.0.15
[89] pillar_1.9.0 grid_4.3.3
[91] vctrs_0.6.5 urlchecker_1.0.1
[93] promises_1.3.0 dbplyr_2.5.0
[95] xtable_1.8-4 evaluate_0.23
[97] GenomicFeatures_1.54.4 cli_3.6.2
[99] compiler_4.3.3 rlang_1.1.3
[101] crayon_1.5.2 fs_1.6.3
[103] stringi_1.8.3 viridisLite_0.4.2
[105] assertthat_0.2.1 munsell_0.5.1
[107] lazyeval_0.2.2 devtools_2.4.5
[109] glmnet_4.1-8 quantreg_5.97
[111] Matrix_1.6-5 hms_1.1.3
[113] bit64_4.0.5 KEGGREST_1.42.0
[115] shiny_1.8.1.1 googleAuthR_2.0.1
[117] iterpc_0.4.2 gargle_1.5.2
[119] broom_1.0.5 memoise_2.0.1
[121] DEoptimR_1.1-3 bit_4.0.5
```