Test SUSIE for regions near genes (500kb flanking)

Last updated: 2020-06-14

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Knit directory: causal-TWAS/

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Rmd	8708f04	simingz	2020-06-11	SUSIE
html	8708f04	simingz	2020-06-11	SUSIE

library(mr.ash.alpha)
library(data.table)
suppressMessages({library(plotly)})

plot_pip <- function(dt){
  pal <- c("salmon", "darkgreen")
  pal <- setNames(pal, c("Causal", "Non causal"))
  
  fig <- plot_ly(dt, x = ~ pos, y = ~ pip, type = 'scatter', mode = 'markers', color = ~ ifcausal, colors = pal, text = ~paste("Name: ", name))

  fig <- fig %>% layout(yaxis = list(title = "PIP"))
  return(fig)
}

plot_all <- function(susieres, mrashres.gene, mrashres.snp){
  dt <- read.table(susieres , header =T)
  
  a <- read.table(mrashres.gene , header =T)
  a[a$ifcausal == 1, "ifcausal"] = "Causal"
  a[a$ifcausal == 0, "ifcausal"] = "Non causal"
  
  dt.gene <- merge(dt, a, by= "name")

  a <- read.table(mrashres.snp , header =T)
  a[a$ifcausal == 1, "ifcausal"] = "Causal"
  a[a$ifcausal == 0, "ifcausal"] = "Non causal"
  
  dt.snp <- merge(dt, a, by= "name")
  
  fig1 <- plot_pip(dt.gene)
  fig2 <- plot_pip(dt.snp)

  fig <- subplot(fig1, fig2, nrows= 2, shareX = T, titleY = T)
  
  fig <- fig %>% layout(autosize = F, width = 600, height = 600, margin = 0.02,
    xaxis = list(title = "Genomic position"))
  
  fig <- fig %>% toWebGL()
  fig
}

simdatadir <- "~/causalTWAS/simulations/simulation_ashtest_20200503/"
outputdir <- "~/causalTWAS/simulations/simulation_susietest_20200604/"
mr.ash2dir <-  "~/causalTWAS/simulations/simulation_ashtest_20200527/"

Simulation 1

Priors:

readLines(paste0(outputdir, "prior-1.R"))

[1] ""                                                                   
[2] "# this is the parameter estimated by mr.ash2 in simulation+20200503"
[3] ""                                                                   
[4] "prior.SNP <- 0.0003892186 "                                         
[5] "prior.gene <- 0.103"

SUSIE results:

mrashtag <- "20200527-1"
susietag <- "20200604-1"
mrashres.gene <- paste0(mr.ash2dir, mrashtag, "-mr.ash2s.expr-res.expr.txt")
mrashres.snp <- paste0(mr.ash2dir, mrashtag, "-mr.ash2s.expr-res.snp.txt")

FALSE positives in mr.ash2

name <- "DGCR14"
susieres <- paste0(outputdir, susietag,"-", name, "-susieres.txt")
print(paste0("SUISE results for regions around ", name))

[1] "SUISE results for regions around DGCR14"

plot_all(susieres, mrashres.gene, mrashres.snp)

Warning: `arrange_()` is deprecated as of dplyr 0.7.0.
Please use `arrange()` instead.
See vignette('programming') for more help
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.

Warning: Specifying width/height in layout() is now deprecated.
Please specify in ggplotly() or plot_ly()

name <- "VPREB3"
susieres <- paste0(outputdir, susietag,"-", name, "-susieres.txt")
print(paste0("SUISE results for regions around ", name))

[1] "SUISE results for regions around VPREB3"

plot_all(susieres, mrashres.gene, mrashres.snp)

Warning: Specifying width/height in layout() is now deprecated.
Please specify in ggplotly() or plot_ly()

name <- "TCN2"
susieres <- paste0(outputdir, susietag,"-", name, "-susieres.txt")
print(paste0("SUISE results for regions around ", name))

[1] "SUISE results for regions around TCN2"

plot_all(susieres, mrashres.gene, mrashres.snp)

Warning: Specifying width/height in layout() is now deprecated.
Please specify in ggplotly() or plot_ly()

FALSE negatives in mr.ash2

name <- "CBX6"
susieres <- paste0(outputdir, susietag,"-", name, "-susieres.txt")
print(paste0("SUISE results for regions around ", name))

[1] "SUISE results for regions around CBX6"

plot_all(susieres, mrashres.gene, mrashres.snp)

Warning: Specifying width/height in layout() is now deprecated.
Please specify in ggplotly() or plot_ly()

name <- "CHEK2"
susieres <- paste0(outputdir, susietag,"-", name, "-susieres.txt")
print(paste0("SUISE results for regions around ", name))

[1] "SUISE results for regions around CHEK2"

plot_all(susieres, mrashres.gene, mrashres.snp)

Warning: Specifying width/height in layout() is now deprecated.
Please specify in ggplotly() or plot_ly()

True positives in mr.ash2

name <- "LMF2"
susieres <- paste0(outputdir, susietag,"-", name, "-susieres.txt")
print(paste0("SUISE results for regions around ", name))

[1] "SUISE results for regions around LMF2"

plot_all(susieres, mrashres.gene, mrashres.snp)

Warning: Specifying width/height in layout() is now deprecated.
Please specify in ggplotly() or plot_ly()

name <- "DDX17"
susieres <- paste0(outputdir, susietag,"-", name, "-susieres.txt")
print(paste0("SUISE results for regions around ", name))

[1] "SUISE results for regions around DDX17"

plot_all(susieres, mrashres.gene, mrashres.snp)

Warning: Specifying width/height in layout() is now deprecated.
Please specify in ggplotly() or plot_ly()

name <- "MIF"
susieres <- paste0(outputdir, susietag,"-", name, "-susieres.txt")
print(paste0("SUISE results for regions around ", name))

[1] "SUISE results for regions around MIF"

plot_all(susieres, mrashres.gene, mrashres.snp)

Warning: Specifying width/height in layout() is now deprecated.
Please specify in ggplotly() or plot_ly()

Simulation 3

Priors:

readLines(paste0(outputdir, "prior-3.R"))

[1] ""                                                                   
[2] "# this is the parameter estimated by mr.ash2 in simulation+20200503"
[3] ""                                                                   
[4] "prior.SNP <- 0.0001854237 "                                         
[5] "prior.gene <- 0.0525"

SUSIE results:

mrashtag <- "20200527-3"
susietag <- "20200604-3"
mrashres.gene <- paste0(mr.ash2dir, mrashtag, "-mr.ash2s.expr-res.expr.txt")
mrashres.snp <- paste0(mr.ash2dir, mrashtag, "-mr.ash2s.expr-res.snp.txt")

name <- "MCM5"
susieres <- paste0(outputdir, susietag,"-", name, "-susieres.txt")
print(paste0("SUISE results for regions around ", name))

[1] "SUISE results for regions around MCM5"

plot_all(susieres, mrashres.gene, mrashres.snp)

Warning: Specifying width/height in layout() is now deprecated.
Please specify in ggplotly() or plot_ly()

name <- "CBX6"
susieres <- paste0(outputdir, susietag,"-", name, "-susieres.txt")
print(paste0("SUISE results for regions around ", name))

[1] "SUISE results for regions around CBX6"

plot_all(susieres, mrashres.gene, mrashres.snp)

Warning: Specifying width/height in layout() is now deprecated.
Please specify in ggplotly() or plot_ly()

sessionInfo()

R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.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] plotly_4.9.2.1     ggplot2_3.3.1      data.table_1.12.7 
[4] mr.ash.alpha_0.1-7

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4.6      compiler_3.5.1    pillar_1.4.4     
 [4] later_0.7.5       git2r_0.26.1      workflowr_1.6.0  
 [7] tools_3.5.1       digest_0.6.25     viridisLite_0.3.0
[10] jsonlite_1.6.1    evaluate_0.12     tibble_3.0.1     
[13] lifecycle_0.2.0   gtable_0.2.0      lattice_0.20-38  
[16] pkgconfig_2.0.2   rlang_0.4.6       Matrix_1.2-15    
[19] shiny_1.2.0       crosstalk_1.0.0   yaml_2.2.0       
[22] httr_1.4.1        withr_2.1.2       dplyr_1.0.0      
[25] stringr_1.4.0     knitr_1.20        htmlwidgets_1.3  
[28] generics_0.0.2    fs_1.3.1          vctrs_0.3.1      
[31] tidyselect_1.1.0  rprojroot_1.3-2   grid_3.5.1       
[34] glue_1.4.1        R6_2.3.0          rmarkdown_1.10   
[37] tidyr_0.8.3       purrr_0.3.4       magrittr_1.5     
[40] whisker_0.3-2     backports_1.1.2   scales_1.0.0     
[43] promises_1.0.1    htmltools_0.3.6   ellipsis_0.3.1   
[46] xtable_1.8-3      mime_0.6          colorspace_1.3-2 
[49] httpuv_1.4.5      stringi_1.3.1     lazyeval_0.2.1   
[52] munsell_0.5.0     crayon_1.3.4