LD Block Analysis
sheng Qian
2023-5-16
Last updated: 2023-05-18
Checks: 6 1
Knit directory: cTWAS_analysis/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 2653427 | sq-96 | 2023-05-17 | update |
| html | 2653427 | sq-96 | 2023-05-17 | update |
| Rmd | 61bc932 | sq-96 | 2023-05-17 | update |
| html | 61bc932 | sq-96 | 2023-05-17 | update |
| Rmd | a2c2f2e | sq-96 | 2023-05-17 | update |
| html | a2c2f2e | sq-96 | 2023-05-17 | update |
| Rmd | e368df3 | sq-96 | 2023-05-17 | update |
| html | e368df3 | sq-96 | 2023-05-17 | update |
| html | 4c5e2b7 | sq-96 | 2023-05-17 | update |
| Rmd | 6baaa95 | sq-96 | 2023-05-16 | update |
| html | 6baaa95 | sq-96 | 2023-05-16 | update |
for(i in index){
genepip <- get_results(i)[[4]]
genepip <- genepip[,c("id","susie_pip")]
genepip1 <- get_results1(i)[[4]]
genepip1 <- genepip1[,c("id","susie_pip")]
aa <- merge(genepip,genepip1,by = "id")
duplicated_genes <- unique(genepip[duplicated(genepip$id),]$id)
#duplicated_df <- aa[aa$id %in% duplicated_genes,]
load(paste0("/project2/mstephens/causalTWAS/simulations/simulation_ctwas_rss_20210416/ukb-s80.45-adi_simu",i,"-pheno.Rd"))
true_genes <- unlist(sapply(1:22, function(x){phenores$batch[[x]]$id.cgene}))
correlation <- cor(aa$susie_pip.x,aa$susie_pip.y)
aa$label <- 1
for(j in 1:dim(aa)[1]){
if(aa[j,"id"] %in% duplicated_genes){
aa[j,"label"] <- 2
}
}
aa$label1 <- 16
for(k in 1:dim(aa)[1]){
if(aa[k,"id"] %in% true_genes){
aa[k,"label1"] <- 17
}
}
plot(aa$susie_pip.y,aa$susie_pip.x,pch=aa$label1,col=aa$label,cex=0.8,xlab = "old pip", ylab = "new pip",main = paste0(i,"(",round(correlation,3),")"))
}
sessionInfo()R version 4.1.0 (2021-05-18)
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
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[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] workflowr_1.7.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.9 highr_0.9 compiler_4.1.0 pillar_1.8.1
[5] bslib_0.4.1 later_1.3.0 git2r_0.30.1 jquerylib_0.1.4
[9] tools_4.1.0 getPass_0.2-2 digest_0.6.31 jsonlite_1.8.4
[13] evaluate_0.19 lifecycle_1.0.3 tibble_3.1.8 pkgconfig_2.0.3
[17] rlang_1.0.6 cli_3.4.1 rstudioapi_0.14 yaml_2.3.6
[21] xfun_0.35 fastmap_1.1.0 httr_1.4.4 stringr_1.5.0
[25] knitr_1.41 sass_0.4.4 fs_1.5.2 vctrs_0.5.1
[29] rprojroot_2.0.3 data.table_1.14.6 glue_1.6.2 R6_2.5.1
[33] processx_3.8.0 fansi_1.0.3 rmarkdown_2.19 callr_3.7.3
[37] magrittr_2.0.3 whisker_0.4.1 ps_1.7.2 promises_1.2.0.1
[41] htmltools_0.5.4 httpuv_1.6.7 utf8_1.2.2 stringi_1.7.8
[45] cachem_1.0.6