GTEx-Flash
Yuxin Zou
2018-2-6
Last updated: 2018-02-06
Code version: dd20a02
GTEx data
data = readRDS('../data/MatrixEQTLSumStats.Portable.Z.rds')
Z = data$test.zFlash:
flash.data = flash_set_data(Z)
f_greedy = flash_add_greedy(flash.data, K=30)
f_b = flash_backfit(flash.data, f_greedy)
saveRDS(list(backfit = f_b, greedy = f_greedy), '../output/GTExVarCol.rds')
Flash again on the loading matrix
flash.loading = flash_set_data(flash_get_l(f_b)[,1:23])
fl_greedy = flash_add_greedy(flash.loading, K=30)
fl_b = flash_backfit(flash.loading, fl_greedy)
saveRDS(list(backfit = fl_b, greedy = fl_greedy), '../output/GTExVarColLoaing_Flash.rds')
There is no latent structure in the flashr loadings matrix.
Session information
sessionInfo()R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.3
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] flashr_0.4-3
loaded via a namespace (and not attached):
[1] compiler_3.4.3 backports_1.1.2 magrittr_1.5 rprojroot_1.2
[5] tools_3.4.3 htmltools_0.3.6 yaml_2.1.16 Rcpp_0.12.15
[9] stringi_1.1.6 rmarkdown_1.8 knitr_1.17 git2r_0.20.0
[13] stringr_1.2.0 digest_0.6.13 evaluate_0.10.1This R Markdown site was created with workflowr