Last updated: 2019-03-03

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    Rmd 28260cb zouyuxin 2019-03-03 wflow_publish(“analysis/SuSiERobust.Rmd”) 

library(susieR)
library(R.utils)

We use the data in susieR package. It is simulated to have exactly 3 non-zero effects.

data(N3finemapping)
b <- N3finemapping$data$true_coef[,1]
R <- cor(N3finemapping$dat$X)
z_scores = N3finemapping$sumstats[1,,1]/N3finemapping$sumstats[2,,1]
plot(z_scores, pch=16, ylab='z scores')
points(which(b!=0),z_scores[which(b!=0)], col=2, pch=16)

fit1 = susie_z(z_scores, R, L=5)
susie_plot(fit1, y = 'PIP', b=b, main=paste0('objective:', round(susie_get_objective(fit1), 2)))

We fit the model with var \(\sigma^2(R + \lambda I)\).

sourceDirectory("~/Documents/GitHub/susieR/inst/code/susiez_fix/")
fit2 = susie_z_general_fix(z_scores, R, L=5, lambda = 1e-8, track_fit = TRUE, verbose = TRUE)
[1] "before estimate sigma objective:-176108.356082106"
[1] "after estimate sigma2 objective:341.575476122518"
[1] "before estimate sigma objective:349.018680645267"
[1] "after estimate sigma2 objective:349.018681622517"
[1] "before estimate sigma objective:349.022409715368"
[1] "after estimate sigma2 objective:349.022409728946"
[1] "before estimate sigma objective:349.022409728946"
[1] "after estimate sigma2 objective:349.022409728946"
susie_plot(fit2, y = 'PIP', b=b, main=paste0('lambda = 1e-8, objective:', round(susie_get_objective(fit2), 2)))

We fit the model with var \(\sigma^2R + \lambda I\).

sourceDirectory("~/Documents/GitHub/susieR/inst/code/susiez_num/")
par(mfrow = c(2, 3))
fit3 = susie_z_general_num(z_scores, R, L=5, lambda = 1e-8, track_fit = TRUE, verbose = TRUE)
[1] "before estimate sigma2 objective:-176108.356082106"
[1] "after estimate sigma2 objective:-176107.431097485"
[1] "before estimate sigma2 objective:-176102.530490343"
[1] "after estimate sigma2 objective:-176102.184350997"
[1] "before estimate sigma2 objective:-176087.167964295"
[1] "after estimate sigma2 objective:-176087.167964295"
[1] "before estimate sigma2 objective:-176080.196067129"
[1] "after estimate sigma2 objective:-176079.74293158"
[1] "before estimate sigma2 objective:-176076.83603438"
[1] "after estimate sigma2 objective:-176076.83603438"
[1] "before estimate sigma2 objective:-176076.495338684"

[1] "after estimate sigma2 objective:-176076.495338684"
[1] "before estimate sigma2 objective:-176076.4809328"
[1] "after estimate sigma2 objective:-176076.4809328"
[1] "before estimate sigma2 objective:-176076.480770257"
[1] "after estimate sigma2 objective:-176076.480770257"
par(mfrow = c(1, 1))

susie_plot(fit3, y = 'PIP', b=b, main=paste0('lambda = 1e-8, objective:', round(susie_get_objective(fit3), 2)))

par(mfrow = c(2, 3))
fit4 = susie_z_general_num(z_scores, R, L=5, lambda = 0.1, track_fit = TRUE, verbose = TRUE)
[1] "before estimate sigma2 objective:-268.382924136224"
[1] "after estimate sigma2 objective:-268.382924136224"
[1] "before estimate sigma2 objective:-263.583517059885"
[1] "after estimate sigma2 objective:-262.582217811463"
[1] "before estimate sigma2 objective:-246.293667680361"
[1] "after estimate sigma2 objective:-244.398921702326"
[1] "before estimate sigma2 objective:-232.726801436096"
[1] "after estimate sigma2 objective:-232.720246921936"
[1] "before estimate sigma2 objective:-229.849008457783"
[1] "after estimate sigma2 objective:-229.849008457783"
[1] "before estimate sigma2 objective:-229.656391292686"

[1] "after estimate sigma2 objective:-229.656391292686"
[1] "before estimate sigma2 objective:-229.649501048445"
[1] "after estimate sigma2 objective:-229.649501048445"
[1] "before estimate sigma2 objective:-229.648954904787"
[1] "after estimate sigma2 objective:-229.648954904787"
par(mfrow = c(1, 1))

susie_plot(fit4, y = 'PIP', b=b, main=paste0('lambda = 0.1, objective:', round(susie_get_objective(fit4), 2)))

Session information

sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.14.3

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/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] R.utils_2.7.0     R.oo_1.22.0       R.methodsS3_1.7.1 susieR_0.6.4.0454

loaded via a namespace (and not attached):
 [1] workflowr_1.1.1 Rcpp_1.0.0      lattice_0.20-38 digest_0.6.18  
 [5] rprojroot_1.3-2 grid_3.5.1      backports_1.1.3 git2r_0.24.0   
 [9] magrittr_1.5    evaluate_0.12   stringi_1.2.4   whisker_0.3-2  
[13] Matrix_1.2-15   rmarkdown_1.11  tools_3.5.1     stringr_1.3.1  
[17] yaml_2.2.0      compiler_3.5.1  htmltools_0.3.6 knitr_1.20

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