GTEx-Flash
Yuxin Zou
2018-2-6
Last updated: 2018-07-14
Code version: cec3828
GTEx data
data = readRDS('../data/MatrixEQTLSumStats.Portable.Z.rds')
Z = data$test.zFlash:
flash.data = flash_set_data(Z)
f_greedy = flash_add_greedy(flash.data, K=30)
f_b = flash_backfit(flash.data, f_greedy)
saveRDS(list(backfit = f_b, greedy = f_greedy), '../output/GTExVarCol.rds')
Flash again on the loading matrix
flash.loading = flash_set_data(flash_get_ldf(f_b)$l[,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')
Session information
sessionInfo()R version 3.4.4 (2018-03-15)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.5
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_0.5-12
loaded via a namespace (and not attached):
[1] Rcpp_0.12.17 bindr_0.1.1 compiler_3.4.4
[4] pillar_1.2.2 git2r_0.21.0 plyr_1.8.4
[7] iterators_1.0.9 tools_3.4.4 digest_0.6.15
[10] evaluate_0.10.1 tibble_1.4.2 gtable_0.2.0
[13] lattice_0.20-35 pkgconfig_2.0.1 rlang_0.2.1
[16] Matrix_1.2-14 foreach_1.4.4 yaml_2.1.19
[19] parallel_3.4.4 bindrcpp_0.2.2 stringr_1.3.0
[22] dplyr_0.7.4 knitr_1.20 rprojroot_1.3-2
[25] grid_3.4.4 glue_1.2.0 R6_2.2.2
[28] rmarkdown_1.9 ggplot2_3.0.0 ashr_2.2-7
[31] magrittr_1.5 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 pscl_1.5.2
[43] doParallel_1.0.11 munsell_0.4.3 truncnorm_1.0-8
[46] SQUAREM_2017.10-1This R Markdown site was created with workflowr