Fine Mapping:

Parkinson’s Disease

# knitr::opts_chunk$set(error = T) # Knit even with errors 
# source("echolocatoR/R/MAIN.R") 
library(dplyr)

library(stringr); library(bsselectR) # devtools::install_github("walkerke/bsselectR")

Nalls et. al. (2019) w/ 23andMe

Summarize Fine-mapping Results

Show all plots

# .tabset-dropdown
loci <- list.dirs("./Data/GWAS/Nalls23andMe_2019", recursive = F) %>% basename()
loci <- loci[loci!="_genome_wide"]
plot.paths <- file.path("./Data/GWAS/Nalls23andMe_2019", 
                        loci, "Multi-finemap",
                        paste0(loci,"_ggbio.png"))

# Add link to plot
  # baseURL <- "https://github.com/RajLabMSSM/Fine_Mapping/blob/master/Data/GWAS/Nalls23andMe_2019"
  # links <- data.frame(Link=file.path(baseURL, top_loci_sort$Locus,"Multi-finemap",
  #           paste0(top_loci_sort$Locus,"_ggbio.png")))
  # top_loci_sort <- cbind(links, top_loci_sort)

# file.path("https://rajlabmssm.github.io/Fine_Mapping/Data/Nalls23andMe_2019",
#           genes,"Multi-finemap", paste0(genes,"_ggbio.png"))
# Dropdown

# genes <-  basename(dirname(dirname(plot.paths)))
# plot.paths <- file.path("https://rajlabmssm.github.io/Fine_Mapping/Data/GWAS/Nalls23andMe_2019",genes,"Multi-finemap",paste0(genes,"_ggbio.png"))
# names(plot.paths) <-  genes
#  
# 
# bsselect(vector = plot.paths, 
#          type = "img", 
#          selected = "LRRK2", 
#          frame_height = "1000", 
#          live_search = T, 
#          show_tick = T)

for (p in plot.paths){
  if(file.exists(p)){
    try({
    gene <- basename(dirname(dirname(p)))
    cat('  \n###', gene, '  \n')
    cat(paste0('![',gene,'](',p,')'))
    cat('  \n')
    })
  }
}

##   
## ### ASXL3   
## ![ASXL3](./Data/GWAS/Nalls23andMe_2019/ASXL3/Multi-finemap/ASXL3_ggbio.png)  
##   
## ### ATG14   
## ![ATG14](./Data/GWAS/Nalls23andMe_2019/ATG14/Multi-finemap/ATG14_ggbio.png)  
##   
## ### ATP6V0A1   
## ![ATP6V0A1](./Data/GWAS/Nalls23andMe_2019/ATP6V0A1/Multi-finemap/ATP6V0A1_ggbio.png)  
##   
## ### BIN3   
## ![BIN3](./Data/GWAS/Nalls23andMe_2019/BIN3/Multi-finemap/BIN3_ggbio.png)  
##   
## ### BRIP1   
## ![BRIP1](./Data/GWAS/Nalls23andMe_2019/BRIP1/Multi-finemap/BRIP1_ggbio.png)  
##   
## ### BST1   
## ![BST1](./Data/GWAS/Nalls23andMe_2019/BST1/Multi-finemap/BST1_ggbio.png)  
##   
## ### C5orf24   
## ![C5orf24](./Data/GWAS/Nalls23andMe_2019/C5orf24/Multi-finemap/C5orf24_ggbio.png)  
##   
## ### CAB39L   
## ![CAB39L](./Data/GWAS/Nalls23andMe_2019/CAB39L/Multi-finemap/CAB39L_ggbio.png)  
##   
## ### CAMK2D   
## ![CAMK2D](./Data/GWAS/Nalls23andMe_2019/CAMK2D/Multi-finemap/CAMK2D_ggbio.png)  
##   
## ### CASC16   
## ![CASC16](./Data/GWAS/Nalls23andMe_2019/CASC16/Multi-finemap/CASC16_ggbio.png)  
##   
## ### CD19   
## ![CD19](./Data/GWAS/Nalls23andMe_2019/CD19/Multi-finemap/CD19_ggbio.png)  
##   
## ### CHRNB1   
## ![CHRNB1](./Data/GWAS/Nalls23andMe_2019/CHRNB1/Multi-finemap/CHRNB1_ggbio.png)  
##   
## ### CLCN3   
## ![CLCN3](./Data/GWAS/Nalls23andMe_2019/CLCN3/Multi-finemap/CLCN3_ggbio.png)  
##   
## ### CRHR1   
## ![CRHR1](./Data/GWAS/Nalls23andMe_2019/CRHR1/Multi-finemap/CRHR1_ggbio.png)  
##   
## ### CRLS1   
## ![CRLS1](./Data/GWAS/Nalls23andMe_2019/CRLS1/Multi-finemap/CRLS1_ggbio.png)  
##   
## ### CTSB   
## ![CTSB](./Data/GWAS/Nalls23andMe_2019/CTSB/Multi-finemap/CTSB_ggbio.png)  
##   
## ### DLG2   
## ![DLG2](./Data/GWAS/Nalls23andMe_2019/DLG2/Multi-finemap/DLG2_ggbio.png)  
##   
## ### DNAH17   
## ![DNAH17](./Data/GWAS/Nalls23andMe_2019/DNAH17/Multi-finemap/DNAH17_ggbio.png)  
##   
## ### DYRK1A   
## ![DYRK1A](./Data/GWAS/Nalls23andMe_2019/DYRK1A/Multi-finemap/DYRK1A_ggbio.png)  
##   
## ### ELOVL7   
## ![ELOVL7](./Data/GWAS/Nalls23andMe_2019/ELOVL7/Multi-finemap/ELOVL7_ggbio.png)  
##   
## ### FAM171A2   
## ![FAM171A2](./Data/GWAS/Nalls23andMe_2019/FAM171A2/Multi-finemap/FAM171A2_ggbio.png)  
##   
## ### FAM47E-STBD1   
## ![FAM47E-STBD1](./Data/GWAS/Nalls23andMe_2019/FAM47E-STBD1/Multi-finemap/FAM47E-STBD1_ggbio.png)  
##   
## ### FAM49B   
## ![FAM49B](./Data/GWAS/Nalls23andMe_2019/FAM49B/Multi-finemap/FAM49B_ggbio.png)  
##   
## ### FBRSL1   
## ![FBRSL1](./Data/GWAS/Nalls23andMe_2019/FBRSL1/Multi-finemap/FBRSL1_ggbio.png)  
##   
## ### FCGR2A   
## ![FCGR2A](./Data/GWAS/Nalls23andMe_2019/FCGR2A/Multi-finemap/FCGR2A_ggbio.png)  
##   
## ### FGF20   
## ![FGF20](./Data/GWAS/Nalls23andMe_2019/FGF20/Multi-finemap/FGF20_ggbio.png)  
##   
## ### FYN   
## ![FYN](./Data/GWAS/Nalls23andMe_2019/FYN/Multi-finemap/FYN_ggbio.png)  
##   
## ### GALC   
## ![GALC](./Data/GWAS/Nalls23andMe_2019/GALC/Multi-finemap/GALC_ggbio.png)  
##   
## ### GBF1   
## ![GBF1](./Data/GWAS/Nalls23andMe_2019/GBF1/Multi-finemap/GBF1_ggbio.png)  
##   
## ### GCH1   
## ![GCH1](./Data/GWAS/Nalls23andMe_2019/GCH1/Multi-finemap/GCH1_ggbio.png)  
##   
## ### GPNMB   
## ![GPNMB](./Data/GWAS/Nalls23andMe_2019/GPNMB/Multi-finemap/GPNMB_ggbio.png)  
##   
## ### GS1-124K5.11   
## ![GS1-124K5.11](./Data/GWAS/Nalls23andMe_2019/GS1-124K5.11/Multi-finemap/GS1-124K5.11_ggbio.png)  
##   
## ### HIP1R   
## ![HIP1R](./Data/GWAS/Nalls23andMe_2019/HIP1R/Multi-finemap/HIP1R_ggbio.png)  
##   
## ### IGSF9B   
## ![IGSF9B](./Data/GWAS/Nalls23andMe_2019/IGSF9B/Multi-finemap/IGSF9B_ggbio.png)  
##   
## ### INPP5F   
## ![INPP5F](./Data/GWAS/Nalls23andMe_2019/INPP5F/Multi-finemap/INPP5F_ggbio.png)  
##   
## ### IP6K2   
## ![IP6K2](./Data/GWAS/Nalls23andMe_2019/IP6K2/Multi-finemap/IP6K2_ggbio.png)  
##   
## ### ITGA8   
## ![ITGA8](./Data/GWAS/Nalls23andMe_2019/ITGA8/Multi-finemap/ITGA8_ggbio.png)  
##   
## ### ITPKB   
## ![ITPKB](./Data/GWAS/Nalls23andMe_2019/ITPKB/Multi-finemap/ITPKB_ggbio.png)  
##   
## ### KCNIP3   
## ![KCNIP3](./Data/GWAS/Nalls23andMe_2019/KCNIP3/Multi-finemap/KCNIP3_ggbio.png)  
##   
## ### KCNS3   
## ![KCNS3](./Data/GWAS/Nalls23andMe_2019/KCNS3/Multi-finemap/KCNS3_ggbio.png)  
##   
## ### KPNA1   
## ![KPNA1](./Data/GWAS/Nalls23andMe_2019/KPNA1/Multi-finemap/KPNA1_ggbio.png)  
##   
## ### KRTCAP2   
## ![KRTCAP2](./Data/GWAS/Nalls23andMe_2019/KRTCAP2/Multi-finemap/KRTCAP2_ggbio.png)  
##   
## ### LCORL   
## ![LCORL](./Data/GWAS/Nalls23andMe_2019/LCORL/Multi-finemap/LCORL_ggbio.png)  
##   
## ### LINC00693   
## ![LINC00693](./Data/GWAS/Nalls23andMe_2019/LINC00693/Multi-finemap/LINC00693_ggbio.png)  
##   
## ### LRRK2   
## ![LRRK2](./Data/GWAS/Nalls23andMe_2019/LRRK2/Multi-finemap/LRRK2_ggbio.png)  
##   
## ### MAP4K4   
## ![MAP4K4](./Data/GWAS/Nalls23andMe_2019/MAP4K4/Multi-finemap/MAP4K4_ggbio.png)  
##   
## ### MBNL2   
## ![MBNL2](./Data/GWAS/Nalls23andMe_2019/MBNL2/Multi-finemap/MBNL2_ggbio.png)  
##   
## ### MCCC1   
## ![MCCC1](./Data/GWAS/Nalls23andMe_2019/MCCC1/Multi-finemap/MCCC1_ggbio.png)  
##   
## ### MED12L   
## ![MED12L](./Data/GWAS/Nalls23andMe_2019/MED12L/Multi-finemap/MED12L_ggbio.png)  
##   
## ### MEX3C   
## ![MEX3C](./Data/GWAS/Nalls23andMe_2019/MEX3C/Multi-finemap/MEX3C_ggbio.png)  
##   
## ### MIPOL1   
## ![MIPOL1](./Data/GWAS/Nalls23andMe_2019/MIPOL1/Multi-finemap/MIPOL1_ggbio.png)  
##   
## ### NOD2   
## ![NOD2](./Data/GWAS/Nalls23andMe_2019/NOD2/Multi-finemap/NOD2_ggbio.png)  
##   
## ### NUCKS1   
## ![NUCKS1](./Data/GWAS/Nalls23andMe_2019/NUCKS1/Multi-finemap/NUCKS1_ggbio.png)  
##   
## ### PAM   
## ![PAM](./Data/GWAS/Nalls23andMe_2019/PAM/Multi-finemap/PAM_ggbio.png)  
##   
## ### RETREG3   
## ![RETREG3](./Data/GWAS/Nalls23andMe_2019/RETREG3/Multi-finemap/RETREG3_ggbio.png)  
##   
## ### RIMS1   
## ![RIMS1](./Data/GWAS/Nalls23andMe_2019/RIMS1/Multi-finemap/RIMS1_ggbio.png)  
##   
## ### RIT2   
## ![RIT2](./Data/GWAS/Nalls23andMe_2019/RIT2/Multi-finemap/RIT2_ggbio.png)  
##   
## ### RNF141   
## ![RNF141](./Data/GWAS/Nalls23andMe_2019/RNF141/Multi-finemap/RNF141_ggbio.png)  
##   
## ### RPS12   
## ![RPS12](./Data/GWAS/Nalls23andMe_2019/RPS12/Multi-finemap/RPS12_ggbio.png)  
##   
## ### RPS6KL1   
## ![RPS6KL1](./Data/GWAS/Nalls23andMe_2019/RPS6KL1/Multi-finemap/RPS6KL1_ggbio.png)  
##   
## ### SATB1   
## ![SATB1](./Data/GWAS/Nalls23andMe_2019/SATB1/Multi-finemap/SATB1_ggbio.png)  
##   
## ### SCAF11   
## ![SCAF11](./Data/GWAS/Nalls23andMe_2019/SCAF11/Multi-finemap/SCAF11_ggbio.png)  
##   
## ### SETD1A   
## ![SETD1A](./Data/GWAS/Nalls23andMe_2019/SETD1A/Multi-finemap/SETD1A_ggbio.png)  
##   
## ### SH3GL2   
## ![SH3GL2](./Data/GWAS/Nalls23andMe_2019/SH3GL2/Multi-finemap/SH3GL2_ggbio.png)  
##   
## ### SIPA1L2   
## ![SIPA1L2](./Data/GWAS/Nalls23andMe_2019/SIPA1L2/Multi-finemap/SIPA1L2_ggbio.png)  
##   
## ### SNCA   
## ![SNCA](./Data/GWAS/Nalls23andMe_2019/SNCA/Multi-finemap/SNCA_ggbio.png)  
##   
## ### SP1   
## ![SP1](./Data/GWAS/Nalls23andMe_2019/SP1/Multi-finemap/SP1_ggbio.png)  
##   
## ### SPPL2B   
## ![SPPL2B](./Data/GWAS/Nalls23andMe_2019/SPPL2B/Multi-finemap/SPPL2B_ggbio.png)  
##   
## ### SPTSSB   
## ![SPTSSB](./Data/GWAS/Nalls23andMe_2019/SPTSSB/Multi-finemap/SPTSSB_ggbio.png)  
##   
## ### STK39   
## ![STK39](./Data/GWAS/Nalls23andMe_2019/STK39/Multi-finemap/STK39_ggbio.png)  
##   
## ### SYT17   
## ![SYT17](./Data/GWAS/Nalls23andMe_2019/SYT17/Multi-finemap/SYT17_ggbio.png)  
##   
## ### TMEM163   
## ![TMEM163](./Data/GWAS/Nalls23andMe_2019/TMEM163/Multi-finemap/TMEM163_ggbio.png)  
##   
## ### TMEM175   
## ![TMEM175](./Data/GWAS/Nalls23andMe_2019/TMEM175/Multi-finemap/TMEM175_ggbio.png)  
##   
## ### UBAP2   
## ![UBAP2](./Data/GWAS/Nalls23andMe_2019/UBAP2/Multi-finemap/UBAP2_ggbio.png)  
##   
## ### VAMP4   
## ![VAMP4](./Data/GWAS/Nalls23andMe_2019/VAMP4/Multi-finemap/VAMP4_ggbio.png)  
##   
## ### VPS13C   
## ![VPS13C](./Data/GWAS/Nalls23andMe_2019/VPS13C/Multi-finemap/VPS13C_ggbio.png)  
##   
## ### WNT3   
## ![WNT3](./Data/GWAS/Nalls23andMe_2019/WNT3/Multi-finemap/WNT3_ggbio.png)

Session Information

sessionInfo()

## R version 3.6.1 (2019-07-05)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS Mojave 10.14.5
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] bsselectR_0.1.0 stringr_1.4.0   dplyr_0.8.3    
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.3        crayon_1.3.4      digest_0.6.23     assertthat_0.2.1 
##  [5] R6_2.4.1          magrittr_1.5      evaluate_0.14     pillar_1.4.3     
##  [9] rlang_0.4.2       stringi_1.4.5     rmarkdown_2.0     tools_3.6.1      
## [13] htmlwidgets_1.5.1 glue_1.3.1        purrr_0.3.3       xfun_0.12        
## [17] yaml_2.2.0        compiler_3.6.1    pkgconfig_2.0.3   htmltools_0.4.0  
## [21] tidyselect_0.2.5  knitr_1.26        tibble_2.1.3

print(paste("susieR ", packageVersion("susieR")))

## [1] "susieR  0.8.0"