log BF calculation

Last updated: 2019-03-12

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library(susieR)
library(R.utils)

Loading required package: R.oo

Loading required package: R.methodsS3

R.methodsS3 v1.7.1 (2016-02-15) successfully loaded. See ?R.methodsS3 for help.

R.oo v1.22.0 (2018-04-21) successfully loaded. See ?R.oo for help.

Attaching package: 'R.oo'

The following objects are masked from 'package:methods':

    getClasses, getMethods

The following objects are masked from 'package:base':

    attach, detach, gc, load, save

R.utils v2.7.0 successfully loaded. See ?R.utils for help.

Attaching package: 'R.utils'

The following object is masked from 'package:utils':

    timestamp

The following objects are masked from 'package:base':

    cat, commandArgs, getOption, inherits, isOpen, parse, warnings

library(mvtnorm)
sourceDirectory('~/Documents/GitHub/susieR/inst/code/susiez_num/')

Using N3finemapping from susieR, we run susie model with lambda 1e-8.

data(N3finemapping)
b <- N3finemapping$data$true_coef[,1]
R <- cor(N3finemapping$dat$X)
z_scores = N3finemapping$sumstats[1,,1]/N3finemapping$sumstats[2,,1]
fit_lbf = susie_z_general_num(z_scores, R, L=1, max_iter = 1, lambda = 0.1, estimate_prior_method = 'EM')

The head of log BF from mvtnorm build-in function is

0.06449783 -0.36519030 -0.09638240 -0.08256167 -0.25397378 -0.31992161

The head of log BF from our computation is

0.22989997 -0.09115324  0.05552693  0.04863540 -0.09050853 -0.09024205

If we run susie model with lambda = 0.1, the log BF from mvtnorm build-in function is same as log BF from our computation.

The head of it is

0.24190347 -0.08910697  0.06196027  0.05362330 -0.08647301 -0.08434728

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] mvtnorm_1.0-8     R.utils_2.7.0     R.oo_1.22.0       R.methodsS3_1.7.1
[5] susieR_0.7.1.0482

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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