Flash on deviation

Last updated: 2018-05-11

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library(flashr); library(colorRamps); library(corrplot); library(mashr)

corrplot 0.84 loaded

Loading required package: ashr

data = readRDS('../data/results/control/CompiledData.rds')

mash.data = mash_set_data(Bhat = data$beta, pval = data$p)

flash.data = flash_set_data(mash.data$Bhat/mash.data$Shat)
flash.model = flash(flash.data, greedy=TRUE, backfit = TRUE)

fitting factor/loading 1

fitting factor/loading 2

fitting factor/loading 3

factors = flash_get_ldf(flash.model)$f
row.names(factors) = colnames(data$beta)
pve.order = order(flash_get_pve(flash.model), decreasing = TRUE)

par(mfrow=c(1,2))
for(i in pve.order){
  barplot(factors[,i], main=paste0('Factor ',i, ' pve= ', round(flash_get_pve(flash.model)[i],3)), las=2, cex.names = 0.7)
}

par(mfrow=c(1,1))

loading = flash.model$EL[, 1:2]
flash.data.l = flash_set_data(loading)
flash.model.l = flash(flash.data.l, greedy = TRUE, backfit = TRUE)

fitting factor/loading 1

Z.center = apply(mash.data$Bhat/mash.data$Shat, 2, function(x) x - mean(x))
flash.data.c = flash_set_data(Z.center)
flash.model.c = flash(flash.data.c, greedy=TRUE, backfit = TRUE)

fitting factor/loading 1

fitting factor/loading 2

fitting factor/loading 3

fitting factor/loading 4

factors = flash_get_ldf(flash.model.c)$f
row.names(factors) = colnames(data$beta)
pve.order = order(flash_get_pve(flash.model.c), decreasing = TRUE)

par(mfrow=c(1,3))
for(i in pve.order){
  barplot(factors[,i], main=paste0('Factor ',i, ' pve= ', round(flash_get_pve(flash.model.c)[i],3)), las=2, cex.names = 0.7)
}

par(mfrow=c(1,1))

loading.c = flash.model.c$EL[, 1:3]
flash.data.lc = flash_set_data(loading.c)
flash.model.lc = flash(flash.data.lc, greedy = TRUE, backfit = TRUE)

fitting factor/loading 1

sessionInfo()

R version 3.4.4 (2018-03-15)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.4

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/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] mashr_0.2-6    ashr_2.2-7     corrplot_0.84  colorRamps_2.3
[5] flashr_0.5-6  

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.16      pillar_1.2.2      compiler_3.4.4   
 [4] git2r_0.21.0      plyr_1.8.4        workflowr_1.0.1  
 [7] R.methodsS3_1.7.1 R.utils_2.6.0     iterators_1.0.9  
[10] tools_3.4.4       digest_0.6.15     tibble_1.4.2     
[13] evaluate_0.10.1   gtable_0.2.0      lattice_0.20-35  
[16] rlang_0.2.0       Matrix_1.2-14     foreach_1.4.4    
[19] yaml_2.1.19       parallel_3.4.4    mvtnorm_1.0-7    
[22] ebnm_0.1-11       stringr_1.3.0     knitr_1.20       
[25] rprojroot_1.3-2   grid_3.4.4        rmarkdown_1.9    
[28] rmeta_3.0         ggplot2_2.2.1     magrittr_1.5     
[31] whisker_0.3-2     backports_1.1.2   scales_0.5.0     
[34] codetools_0.2-15  htmltools_0.3.6   MASS_7.3-50      
[37] assertthat_0.2.0  softImpute_1.4    colorspace_1.3-2 
[40] stringi_1.2.2     lazyeval_0.2.1    doParallel_1.0.11
[43] pscl_1.5.2        munsell_0.4.3     truncnorm_1.0-8  
[46] SQUAREM_2017.10-1 R.oo_1.22.0      

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