Last updated: 2018-08-30
workflowr checks: (Click a bullet for more information) ✔ R Markdown file: up-to-date
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✔ Seed:
set.seed(20180719)
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was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.
✔ Session information: recorded
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✔ Repository version: e5fe6e0
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File | Version | Author | Date | Message |
---|---|---|---|---|
Rmd | e5fe6e0 | Xiang Zhu | 2018-08-30 | wflow_publish(“analysis/load2013_liver.Rmd”) |
/project/mstephens/test_rss/data/load2013/load2013_sumstat.mat
/scratch/PI/whwong/zduren/share/PECA_human/PECA2/Liver_network.txt
res <- R.matlab::readMat("~/Dropbox/rss/Data/peca_human/out_market/load2013_liver_out.mat")
# create a data frame for ELBO
elbo_df <- data.frame(
piva <- c(res$piva),
sigb <- c(res$sigb),
elbo <- c(res$vb.elbo),
time <- c(res$exe.time)
)
names(elbo_df) <- c("piva","sigb","elbo","time")
elbo_df$posp <- normalize_logw(elbo_df$elbo)
map_id <- which.max(elbo_df$elbo)
map_id <- 1
gene_df <- data.frame(vb_weight=res$vb.weight[, map_id],
vb_mean=res$vb.mean[, map_id],
vb_var=res$vb.var[, map_id],
gene_nid=1:dim(res$vb.weight)[1])
gene_info <- readRDS("~/Dropbox/rss/Data/peca_human/data_factory/20180820/Homo_sapiens_GRCh37_gene_info.rds")
gene_df <- dplyr::inner_join(gene_info[,c("hgnc_symbol","chromosome_name","start_position","end_position","gene_nid")], gene_df, by="gene_nid")
gene_df <- dplyr::arrange(gene_df, -vb_weight, -vb_mean)
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6
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] bindrcpp_0.2.2 dplyr_0.7.5 R.matlab_3.6.1
loaded via a namespace (and not attached):
[1] Rcpp_0.12.17 knitr_1.20 bindr_0.1.1
[4] whisker_0.3-2 magrittr_1.5 workflowr_1.1.1
[7] tidyselect_0.2.4 R6_2.2.2 rlang_0.2.1
[10] stringr_1.3.1 tools_3.5.1 R.oo_1.22.0
[13] git2r_0.21.0 htmltools_0.3.6 yaml_2.1.19
[16] rprojroot_1.3-2 digest_0.6.15 assertthat_0.2.0
[19] tibble_1.4.2 purrr_0.2.5 R.utils_2.6.0
[22] glue_1.2.0 evaluate_0.10.1 rmarkdown_1.10
[25] stringi_1.2.3 pillar_1.2.3 compiler_3.5.1
[28] backports_1.1.2 R.methodsS3_1.7.1 pkgconfig_2.0.1
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