Last updated: 2020-03-01
Checks: 7 0
Knit directory: mmbr-rss-dsc/
This reproducible R Markdown analysis was created with workflowr (version 1.6.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.
The command set.seed(20200227) 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.
Great job! Recording the operating system, R version, and package versions is critical for reproducibility.
Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.
Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated.
Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
Untracked files:
Untracked: analysis/mmbr_rss_simulation_1_problem.Rmd
Untracked: data/lite_data_6.rds
Untracked: data/lite_data_6_shared_1.pkl
Untracked: data/lite_data_6_shared_1_get_sumstats_1.rds
Untracked: data/lite_data_6_shared_1_get_sumstats_1_oracle_generator_1_mnm_rss_shared_16.rds
Untracked: output/mnm_rss_lite_output.20200227.rds
Untracked: output/mnm_rss_lite_output.20200229.rds
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
These are the previous versions of the R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 4ae7d79 | zouyuxin | 2020-03-01 | wflow_publish(“analysis/mmbr_rss_simulation_1.Rmd”) |
| html | 78b6788 | zouyuxin | 2020-03-01 | Build site. |
| html | 8e52256 | zouyuxin | 2020-02-29 | Build site. |
| html | 31cfb3e | zouyuxin | 2020-02-29 | Build site. |
| Rmd | 5ac2293 | zouyuxin | 2020-02-29 | wflow_publish(“analysis/mmbr_rss_simulation_1.Rmd”) |
| html | 7fbc900 | zouyuxin | 2020-02-29 | Build site. |
| Rmd | ae502cd | zouyuxin | 2020-02-29 | wflow_publish(“analysis/mmbr_rss_simulation_1.Rmd”) |
| html | 6d7bf2d | zouyuxin | 2020-02-28 | Build site. |
| Rmd | d5a7ede | zouyuxin | 2020-02-28 | wflow_publish(“analysis/mmbr_rss_simulation_1.Rmd”) |
This is result from our first M&M RSS simulation.
There are 200 data sets, each with 1 causal SNP shared across conditions. The number of conditions are 5 and 10.
library(dplyr)
library(kableExtra)
library(knitr)
out = readRDS('output/mnm_rss_lite_output.20200229.rds')res = out[,-1]
colnames(res) = c('n_traits', 'method', 'resid_method', 'L', 'prior.scale','total', 'valid', 'size', 'purity', 'top_hit', 'total_true', 'total_true_included', 'overlap_var', 'overlap_cs', 'false_positive_cross_cond', 'false_negative_cross_cond', 'true_positive_cross_cond', 'converged', 'filename')
res$resid_method[res$resid_method == 'diag'] = 'identity'
res.prior.simulated = res %>% filter(prior.scale == 'simulated' | is.na(prior.scale))
res.prior.size = res %>% filter(prior.scale == 'size' | is.na(prior.scale))
res.prior.oracle = res %>% filter(prior.scale == 'oracle' | is.na(prior.scale))
rm(out)purity = aggregate(purity~n_traits + resid_method + method + L, res.prior.simulated, mean)
purity = purity[order(purity$n_traits, purity$L),]
rownames(purity) = NULL
knitr::kable(purity) %>% kable_styling(full_width = F) %>%
row_spec(c(7:12, 19:24, 31:36), background = "wheat")| n_traits | resid_method | method | L | purity |
|---|---|---|---|---|
| 5 | all | mnm_rss_shared | 1 | 0.1655099 |
| 5 | identity | mnm_rss_shared | 1 | 0.9856530 |
| 5 | null | mnm_rss_shared | 1 | 0.9007187 |
| 5 | oracle | mnm_rss_shared | 1 | 0.9879269 |
| 5 | flash | mnm_shared | 1 | 0.9941027 |
| 5 | oracle | mnm_shared | 1 | 0.9965768 |
| 5 | all | mnm_rss_shared | 2 | 0.1481444 |
| 5 | identity | mnm_rss_shared | 2 | 0.9659861 |
| 5 | null | mnm_rss_shared | 2 | 0.8563740 |
| 5 | oracle | mnm_rss_shared | 2 | 0.9699972 |
| 5 | flash | mnm_shared | 2 | 0.9941027 |
| 5 | oracle | mnm_shared | 2 | 0.9965768 |
| 5 | all | mnm_rss_shared | 10 | 0.0659099 |
| 5 | identity | mnm_rss_shared | 10 | 0.2548392 |
| 5 | null | mnm_rss_shared | 10 | 0.2255097 |
| 5 | oracle | mnm_rss_shared | 10 | 0.3947844 |
| 5 | flash | mnm_shared | 10 | 0.9941027 |
| 5 | oracle | mnm_shared | 10 | 0.9965768 |
| 10 | all | mnm_rss_shared | 1 | 0.4304852 |
| 10 | identity | mnm_rss_shared | 1 | 0.9891525 |
| 10 | null | mnm_rss_shared | 1 | 0.9832247 |
| 10 | oracle | mnm_rss_shared | 1 | 0.9899473 |
| 10 | flash | mnm_shared | 1 | 0.9965968 |
| 10 | oracle | mnm_shared | 1 | 0.9986715 |
| 10 | all | mnm_rss_shared | 2 | 0.3704374 |
| 10 | identity | mnm_rss_shared | 2 | 0.9796532 |
| 10 | null | mnm_rss_shared | 2 | 0.9734047 |
| 10 | oracle | mnm_rss_shared | 2 | 0.9842392 |
| 10 | flash | mnm_shared | 2 | 0.9965968 |
| 10 | oracle | mnm_shared | 2 | 0.9986715 |
| 10 | all | mnm_rss_shared | 10 | 0.2043153 |
| 10 | identity | mnm_rss_shared | 10 | 0.9216859 |
| 10 | null | mnm_rss_shared | 10 | 0.8481309 |
| 10 | oracle | mnm_rss_shared | 10 | 0.9384956 |
| 10 | flash | mnm_shared | 10 | 0.9965968 |
| 10 | oracle | mnm_shared | 10 | 0.9986715 |
total_true_included = aggregate(total_true_included ~ n_traits + resid_method + method + L, res.prior.simulated, sum)
total_true = aggregate(total_true ~ n_traits + resid_method + method + L, res.prior.simulated, sum)
cs_overlap = aggregate(overlap_cs ~ n_traits + resid_method + method + L, res.prior.simulated, sum)
snp_overlap = aggregate(overlap_var ~ n_traits + resid_method + method + L, res.prior.simulated, sum)
power = merge(total_true_included, total_true, by = c( 'n_traits' , 'resid_method' , 'method' , 'L'))
power = merge(power, cs_overlap, by = c( 'n_traits' , 'resid_method' , 'method' , 'L'))
power = merge(power, snp_overlap, by = c( 'n_traits' , 'resid_method' , 'method' , 'L'))
power$power = round(power$total_true_included/power$total_true,3)
power$overlap_cs = round(power$overlap_cs, 3)
power$overlap_var = round(power$overlap_var, 3)
power = power[order(power$n_traits, power$L, power$method),]
rownames(power) = NULL
knitr::kable(power) %>% kable_styling(full_width = F) %>%
row_spec(c(7:12, 19:24, 31:36), background = "wheat")| n_traits | resid_method | method | L | total_true_included | total_true | overlap_cs | overlap_var | power |
|---|---|---|---|---|---|---|---|---|
| 5 | all | mnm_rss_shared | 1 | 17 | 200 | 0 | 0 | 0.085 |
| 5 | identity | mnm_rss_shared | 1 | 199 | 200 | 0 | 0 | 0.995 |
| 5 | null | mnm_rss_shared | 1 | 178 | 200 | 0 | 0 | 0.890 |
| 5 | oracle | mnm_rss_shared | 1 | 199 | 200 | 0 | 0 | 0.995 |
| 5 | flash | mnm_shared | 1 | 198 | 200 | 0 | 0 | 0.990 |
| 5 | oracle | mnm_shared | 1 | 195 | 200 | 0 | 0 | 0.975 |
| 5 | all | mnm_rss_shared | 2 | 13 | 200 | 1 | 1 | 0.065 |
| 5 | identity | mnm_rss_shared | 2 | 199 | 200 | 1 | 18 | 0.995 |
| 5 | null | mnm_rss_shared | 2 | 172 | 200 | 3 | 41 | 0.860 |
| 5 | oracle | mnm_rss_shared | 2 | 199 | 200 | 2 | 52 | 0.995 |
| 5 | flash | mnm_shared | 2 | 198 | 200 | 0 | 0 | 0.990 |
| 5 | oracle | mnm_shared | 2 | 195 | 200 | 0 | 0 | 0.975 |
| 5 | all | mnm_rss_shared | 10 | 3 | 200 | 0 | 0 | 0.015 |
| 5 | identity | mnm_rss_shared | 10 | 68 | 200 | 267 | 12340 | 0.340 |
| 5 | null | mnm_rss_shared | 10 | 50 | 200 | 191 | 8724 | 0.250 |
| 5 | oracle | mnm_rss_shared | 10 | 104 | 200 | 465 | 17077 | 0.520 |
| 5 | flash | mnm_shared | 10 | 198 | 200 | 0 | 0 | 0.990 |
| 5 | oracle | mnm_shared | 10 | 195 | 200 | 0 | 0 | 0.975 |
| 10 | all | mnm_rss_shared | 1 | 32 | 200 | 0 | 0 | 0.160 |
| 10 | identity | mnm_rss_shared | 1 | 194 | 200 | 0 | 0 | 0.970 |
| 10 | null | mnm_rss_shared | 1 | 165 | 200 | 0 | 0 | 0.825 |
| 10 | oracle | mnm_rss_shared | 1 | 193 | 200 | 0 | 0 | 0.965 |
| 10 | flash | mnm_shared | 1 | 200 | 200 | 0 | 0 | 1.000 |
| 10 | oracle | mnm_shared | 1 | 198 | 200 | 0 | 0 | 0.990 |
| 10 | all | mnm_rss_shared | 2 | 24 | 200 | 5 | 105 | 0.120 |
| 10 | identity | mnm_rss_shared | 2 | 197 | 200 | 6 | 120 | 0.985 |
| 10 | null | mnm_rss_shared | 2 | 170 | 200 | 9 | 137 | 0.850 |
| 10 | oracle | mnm_rss_shared | 2 | 197 | 200 | 12 | 168 | 0.985 |
| 10 | flash | mnm_shared | 2 | 200 | 200 | 0 | 0 | 1.000 |
| 10 | oracle | mnm_shared | 2 | 198 | 200 | 0 | 0 | 0.990 |
| 10 | all | mnm_rss_shared | 10 | 11 | 200 | 3 | 17 | 0.055 |
| 10 | identity | mnm_rss_shared | 10 | 194 | 200 | 276 | 5802 | 0.970 |
| 10 | null | mnm_rss_shared | 10 | 159 | 200 | 215 | 4618 | 0.795 |
| 10 | oracle | mnm_rss_shared | 10 | 196 | 200 | 209 | 4062 | 0.980 |
| 10 | flash | mnm_shared | 10 | 200 | 200 | 0 | 0 | 1.000 |
| 10 | oracle | mnm_shared | 10 | 198 | 200 | 0 | 0 | 0.990 |
valid = aggregate(valid ~ n_traits + resid_method + method + L, res.prior.simulated, sum)
total = aggregate(total ~ n_traits + resid_method + method + L, res.prior.simulated, sum)
fdr = merge(valid, total, by = c( 'n_traits' , 'resid_method' , 'method', 'L'))
fdr$fdr = round((fdr$total - fdr$valid)/fdr$total,3)
fdr = fdr[order(fdr$n_traits, fdr$L, fdr$method),]
rownames(fdr) = NULL
knitr::kable(fdr) %>% kable_styling(full_width = F) %>%
row_spec(c(7:12, 19:24, 31:36), background = "wheat")| n_traits | resid_method | method | L | valid | total | fdr |
|---|---|---|---|---|---|---|
| 5 | all | mnm_rss_shared | 1 | 17 | 37 | 0.541 |
| 5 | identity | mnm_rss_shared | 1 | 199 | 200 | 0.005 |
| 5 | null | mnm_rss_shared | 1 | 178 | 188 | 0.053 |
| 5 | oracle | mnm_rss_shared | 1 | 199 | 200 | 0.005 |
| 5 | flash | mnm_shared | 1 | 198 | 200 | 0.010 |
| 5 | oracle | mnm_shared | 1 | 195 | 200 | 0.025 |
| 5 | all | mnm_rss_shared | 2 | 14 | 40 | 0.650 |
| 5 | identity | mnm_rss_shared | 2 | 200 | 200 | 0.000 |
| 5 | null | mnm_rss_shared | 2 | 175 | 190 | 0.079 |
| 5 | oracle | mnm_rss_shared | 2 | 201 | 201 | 0.000 |
| 5 | flash | mnm_shared | 2 | 198 | 200 | 0.010 |
| 5 | oracle | mnm_shared | 2 | 195 | 200 | 0.025 |
| 5 | all | mnm_rss_shared | 10 | 3 | 83 | 0.964 |
| 5 | identity | mnm_rss_shared | 10 | 190 | 190 | 0.000 |
| 5 | null | mnm_rss_shared | 10 | 130 | 190 | 0.316 |
| 5 | oracle | mnm_rss_shared | 10 | 311 | 311 | 0.000 |
| 5 | flash | mnm_shared | 10 | 198 | 200 | 0.010 |
| 5 | oracle | mnm_shared | 10 | 195 | 200 | 0.025 |
| 10 | all | mnm_rss_shared | 1 | 32 | 94 | 0.660 |
| 10 | identity | mnm_rss_shared | 1 | 194 | 199 | 0.025 |
| 10 | null | mnm_rss_shared | 1 | 165 | 198 | 0.167 |
| 10 | oracle | mnm_rss_shared | 1 | 193 | 199 | 0.030 |
| 10 | flash | mnm_shared | 1 | 200 | 200 | 0.000 |
| 10 | oracle | mnm_shared | 1 | 198 | 200 | 0.010 |
| 10 | all | mnm_rss_shared | 2 | 27 | 100 | 0.730 |
| 10 | identity | mnm_rss_shared | 2 | 203 | 204 | 0.005 |
| 10 | null | mnm_rss_shared | 2 | 177 | 239 | 0.259 |
| 10 | oracle | mnm_rss_shared | 2 | 209 | 211 | 0.009 |
| 10 | flash | mnm_shared | 2 | 200 | 200 | 0.000 |
| 10 | oracle | mnm_shared | 2 | 198 | 200 | 0.010 |
| 10 | all | mnm_rss_shared | 10 | 13 | 160 | 0.919 |
| 10 | identity | mnm_rss_shared | 10 | 349 | 349 | 0.000 |
| 10 | null | mnm_rss_shared | 10 | 269 | 590 | 0.544 |
| 10 | oracle | mnm_rss_shared | 10 | 313 | 313 | 0.000 |
| 10 | flash | mnm_shared | 10 | 200 | 200 | 0.000 |
| 10 | oracle | mnm_shared | 10 | 198 | 200 | 0.010 |
elbo_converged = aggregate(converged~n_traits + resid_method + method + L, res.prior.simulated, mean)
elbo_converged = elbo_converged[which(elbo_converged$L!=1),]
elbo_converged = elbo_converged[order(elbo_converged$n_traits),]
rownames(elbo_converged) = NULL
knitr::kable(elbo_converged) %>% kable_styling(full_width = F) %>%
row_spec(c(7:12, 19:24), background = "wheat")| n_traits | resid_method | method | L | converged |
|---|---|---|---|---|
| 5 | all | mnm_rss_shared | 2 | 1.000 |
| 5 | identity | mnm_rss_shared | 2 | 1.000 |
| 5 | null | mnm_rss_shared | 2 | 1.000 |
| 5 | oracle | mnm_rss_shared | 2 | 1.000 |
| 5 | flash | mnm_shared | 2 | 0.955 |
| 5 | oracle | mnm_shared | 2 | 0.930 |
| 5 | all | mnm_rss_shared | 10 | 1.000 |
| 5 | identity | mnm_rss_shared | 10 | 0.700 |
| 5 | null | mnm_rss_shared | 10 | 0.855 |
| 5 | oracle | mnm_rss_shared | 10 | 0.505 |
| 5 | flash | mnm_shared | 10 | 0.955 |
| 5 | oracle | mnm_shared | 10 | 0.930 |
| 10 | all | mnm_rss_shared | 2 | 1.000 |
| 10 | identity | mnm_rss_shared | 2 | 1.000 |
| 10 | null | mnm_rss_shared | 2 | 1.000 |
| 10 | oracle | mnm_rss_shared | 2 | 1.000 |
| 10 | flash | mnm_shared | 2 | 0.915 |
| 10 | oracle | mnm_shared | 2 | 0.905 |
| 10 | all | mnm_rss_shared | 10 | 0.980 |
| 10 | identity | mnm_rss_shared | 10 | 0.030 |
| 10 | null | mnm_rss_shared | 10 | 0.510 |
| 10 | oracle | mnm_rss_shared | 10 | 0.020 |
| 10 | flash | mnm_shared | 10 | 0.915 |
| 10 | oracle | mnm_shared | 10 | 0.905 |
purity = aggregate(purity~n_traits + resid_method + method + L, res.prior.size, mean)
purity = purity[order(purity$n_traits, purity$L),]
rownames(purity) = NULL
knitr::kable(purity) %>% kable_styling(full_width = F) %>%
row_spec(c(7:12, 19:24, 31:36), background = "wheat")| n_traits | resid_method | method | L | purity |
|---|---|---|---|---|
| 5 | all | mnm_rss_shared | 1 | 0.9253474 |
| 5 | identity | mnm_rss_shared | 1 | 0.9960291 |
| 5 | null | mnm_rss_shared | 1 | 0.9831272 |
| 5 | oracle | mnm_rss_shared | 1 | 0.9962116 |
| 5 | flash | mnm_shared | 1 | 0.9941027 |
| 5 | oracle | mnm_shared | 1 | 0.9965768 |
| 5 | all | mnm_rss_shared | 2 | 0.9883732 |
| 5 | identity | mnm_rss_shared | 2 | 0.9936497 |
| 5 | null | mnm_rss_shared | 2 | 0.9792400 |
| 5 | oracle | mnm_rss_shared | 2 | 0.9924485 |
| 5 | flash | mnm_shared | 2 | 0.9941027 |
| 5 | oracle | mnm_shared | 2 | 0.9965768 |
| 5 | all | mnm_rss_shared | 10 | 0.9976531 |
| 5 | identity | mnm_rss_shared | 10 | 0.9934514 |
| 5 | null | mnm_rss_shared | 10 | 0.9829585 |
| 5 | oracle | mnm_rss_shared | 10 | 0.9914243 |
| 5 | flash | mnm_shared | 10 | 0.9941027 |
| 5 | oracle | mnm_shared | 10 | 0.9965768 |
| 10 | all | mnm_rss_shared | 1 | 0.9608779 |
| 10 | identity | mnm_rss_shared | 1 | 0.9975859 |
| 10 | null | mnm_rss_shared | 1 | 0.9958050 |
| 10 | oracle | mnm_rss_shared | 1 | 0.9977314 |
| 10 | flash | mnm_shared | 1 | 0.9965968 |
| 10 | oracle | mnm_shared | 1 | 0.9986715 |
| 10 | all | mnm_rss_shared | 2 | 0.9978111 |
| 10 | identity | mnm_rss_shared | 2 | 0.9951683 |
| 10 | null | mnm_rss_shared | 2 | 0.9899097 |
| 10 | oracle | mnm_rss_shared | 2 | 0.9964637 |
| 10 | flash | mnm_shared | 2 | 0.9965968 |
| 10 | oracle | mnm_shared | 2 | 0.9986715 |
| 10 | all | mnm_rss_shared | 10 | 1.0000000 |
| 10 | identity | mnm_rss_shared | 10 | 0.9958573 |
| 10 | null | mnm_rss_shared | 10 | 0.9944488 |
| 10 | oracle | mnm_rss_shared | 10 | 0.9950210 |
| 10 | flash | mnm_shared | 10 | 0.9965968 |
| 10 | oracle | mnm_shared | 10 | 0.9986715 |
total_true_included = aggregate(total_true_included ~ n_traits + resid_method + method + L, res.prior.size, sum)
total_true = aggregate(total_true ~ n_traits + resid_method + method + L, res.prior.size, sum)
cs_overlap = aggregate(overlap_cs ~ n_traits + resid_method + method + L, res.prior.size, sum)
snp_overlap = aggregate(overlap_var ~ n_traits + resid_method + method + L, res.prior.size, sum)
power = merge(total_true_included, total_true, by = c( 'n_traits' , 'resid_method' , 'method' , 'L'))
power = merge(power, cs_overlap, by = c( 'n_traits' , 'resid_method' , 'method' , 'L'))
power = merge(power, snp_overlap, by = c( 'n_traits' , 'resid_method' , 'method' , 'L'))
power$power = round(power$total_true_included/power$total_true,3)
power$overlap_cs = round(power$overlap_cs, 3)
power$overlap_var = round(power$overlap_var, 3)
power = power[order(power$n_traits, power$L, power$method),]
rownames(power) = NULL
knitr::kable(power) %>% kable_styling(full_width = F) %>%
row_spec(c(7:12, 19:24, 31:36), background = "wheat")| n_traits | resid_method | method | L | total_true_included | total_true | overlap_cs | overlap_var | power |
|---|---|---|---|---|---|---|---|---|
| 5 | all | mnm_rss_shared | 1 | 49 | 200 | 0 | 0 | 0.245 |
| 5 | identity | mnm_rss_shared | 1 | 192 | 200 | 0 | 0 | 0.960 |
| 5 | null | mnm_rss_shared | 1 | 168 | 200 | 0 | 0 | 0.840 |
| 5 | oracle | mnm_rss_shared | 1 | 191 | 200 | 0 | 0 | 0.955 |
| 5 | flash | mnm_shared | 1 | 198 | 200 | 0 | 0 | 0.990 |
| 5 | oracle | mnm_shared | 1 | 195 | 200 | 0 | 0 | 0.975 |
| 5 | all | mnm_rss_shared | 2 | 57 | 200 | 0 | 0 | 0.285 |
| 5 | identity | mnm_rss_shared | 2 | 193 | 200 | 5 | 41 | 0.965 |
| 5 | null | mnm_rss_shared | 2 | 169 | 200 | 2 | 35 | 0.845 |
| 5 | oracle | mnm_rss_shared | 2 | 192 | 200 | 8 | 50 | 0.960 |
| 5 | flash | mnm_shared | 2 | 198 | 200 | 0 | 0 | 0.990 |
| 5 | oracle | mnm_shared | 2 | 195 | 200 | 0 | 0 | 0.975 |
| 5 | all | mnm_rss_shared | 10 | 70 | 200 | 3 | 5 | 0.350 |
| 5 | identity | mnm_rss_shared | 10 | 192 | 200 | 7 | 191 | 0.960 |
| 5 | null | mnm_rss_shared | 10 | 170 | 200 | 7 | 151 | 0.850 |
| 5 | oracle | mnm_rss_shared | 10 | 192 | 200 | 8 | 162 | 0.960 |
| 5 | flash | mnm_shared | 10 | 198 | 200 | 0 | 0 | 0.990 |
| 5 | oracle | mnm_shared | 10 | 195 | 200 | 0 | 0 | 0.975 |
| 10 | all | mnm_rss_shared | 1 | 42 | 200 | 0 | 0 | 0.210 |
| 10 | identity | mnm_rss_shared | 1 | 187 | 200 | 0 | 0 | 0.935 |
| 10 | null | mnm_rss_shared | 1 | 155 | 200 | 0 | 0 | 0.775 |
| 10 | oracle | mnm_rss_shared | 1 | 187 | 200 | 0 | 0 | 0.935 |
| 10 | flash | mnm_shared | 1 | 200 | 200 | 0 | 0 | 1.000 |
| 10 | oracle | mnm_shared | 1 | 198 | 200 | 0 | 0 | 0.990 |
| 10 | all | mnm_rss_shared | 2 | 48 | 200 | 0 | 0 | 0.240 |
| 10 | identity | mnm_rss_shared | 2 | 187 | 200 | 12 | 107 | 0.935 |
| 10 | null | mnm_rss_shared | 2 | 154 | 200 | 4 | 35 | 0.770 |
| 10 | oracle | mnm_rss_shared | 2 | 187 | 200 | 12 | 101 | 0.935 |
| 10 | flash | mnm_shared | 2 | 200 | 200 | 0 | 0 | 1.000 |
| 10 | oracle | mnm_shared | 2 | 198 | 200 | 0 | 0 | 0.990 |
| 10 | all | mnm_rss_shared | 10 | 50 | 200 | 0 | 0 | 0.250 |
| 10 | identity | mnm_rss_shared | 10 | 187 | 200 | 40 | 879 | 0.935 |
| 10 | null | mnm_rss_shared | 10 | 154 | 200 | 32 | 660 | 0.770 |
| 10 | oracle | mnm_rss_shared | 10 | 187 | 200 | 28 | 520 | 0.935 |
| 10 | flash | mnm_shared | 10 | 200 | 200 | 0 | 0 | 1.000 |
| 10 | oracle | mnm_shared | 10 | 198 | 200 | 0 | 0 | 0.990 |
valid = aggregate(valid ~ n_traits + resid_method + method + L, res.prior.size, sum)
total = aggregate(total ~ n_traits + resid_method + method + L, res.prior.size, sum)
fdr = merge(valid, total, by = c( 'n_traits' , 'resid_method' , 'method', 'L'))
fdr$fdr = round((fdr$total - fdr$valid)/fdr$total,3)
fdr = fdr[order(fdr$n_traits, fdr$L, fdr$method),]
rownames(fdr) = NULL
knitr::kable(fdr) %>% kable_styling(full_width = F) %>%
row_spec(c(7:12, 19:24, 31:36), background = "wheat")| n_traits | resid_method | method | L | valid | total | fdr |
|---|---|---|---|---|---|---|
| 5 | all | mnm_rss_shared | 1 | 49 | 188 | 0.739 |
| 5 | identity | mnm_rss_shared | 1 | 192 | 200 | 0.040 |
| 5 | null | mnm_rss_shared | 1 | 168 | 200 | 0.160 |
| 5 | oracle | mnm_rss_shared | 1 | 191 | 200 | 0.045 |
| 5 | flash | mnm_shared | 1 | 198 | 200 | 0.010 |
| 5 | oracle | mnm_shared | 1 | 195 | 200 | 0.025 |
| 5 | all | mnm_rss_shared | 2 | 57 | 376 | 0.848 |
| 5 | identity | mnm_rss_shared | 2 | 197 | 205 | 0.039 |
| 5 | null | mnm_rss_shared | 2 | 171 | 270 | 0.367 |
| 5 | oracle | mnm_rss_shared | 2 | 199 | 209 | 0.048 |
| 5 | flash | mnm_shared | 2 | 198 | 200 | 0.010 |
| 5 | oracle | mnm_shared | 2 | 195 | 200 | 0.025 |
| 5 | all | mnm_rss_shared | 10 | 70 | 1805 | 0.961 |
| 5 | identity | mnm_rss_shared | 10 | 197 | 205 | 0.039 |
| 5 | null | mnm_rss_shared | 10 | 173 | 517 | 0.665 |
| 5 | oracle | mnm_rss_shared | 10 | 197 | 207 | 0.048 |
| 5 | flash | mnm_shared | 10 | 198 | 200 | 0.010 |
| 5 | oracle | mnm_shared | 10 | 195 | 200 | 0.025 |
| 10 | all | mnm_rss_shared | 1 | 42 | 193 | 0.782 |
| 10 | identity | mnm_rss_shared | 1 | 187 | 200 | 0.065 |
| 10 | null | mnm_rss_shared | 1 | 155 | 200 | 0.225 |
| 10 | oracle | mnm_rss_shared | 1 | 187 | 200 | 0.065 |
| 10 | flash | mnm_shared | 1 | 200 | 200 | 0.000 |
| 10 | oracle | mnm_shared | 1 | 198 | 200 | 0.010 |
| 10 | all | mnm_rss_shared | 2 | 48 | 384 | 0.875 |
| 10 | identity | mnm_rss_shared | 2 | 199 | 212 | 0.061 |
| 10 | null | mnm_rss_shared | 2 | 158 | 297 | 0.468 |
| 10 | oracle | mnm_rss_shared | 2 | 199 | 212 | 0.061 |
| 10 | flash | mnm_shared | 2 | 200 | 200 | 0.000 |
| 10 | oracle | mnm_shared | 2 | 198 | 200 | 0.010 |
| 10 | all | mnm_rss_shared | 10 | 50 | 1927 | 0.974 |
| 10 | identity | mnm_rss_shared | 10 | 205 | 218 | 0.060 |
| 10 | null | mnm_rss_shared | 10 | 166 | 888 | 0.813 |
| 10 | oracle | mnm_rss_shared | 10 | 202 | 215 | 0.060 |
| 10 | flash | mnm_shared | 10 | 200 | 200 | 0.000 |
| 10 | oracle | mnm_shared | 10 | 198 | 200 | 0.010 |
elbo_converged = aggregate(converged~n_traits + resid_method + method + L, res.prior.size, mean)
elbo_converged = elbo_converged[which(elbo_converged$L!=1),]
elbo_converged = elbo_converged[order(elbo_converged$n_traits),]
rownames(elbo_converged) = NULL
knitr::kable(elbo_converged) %>% kable_styling(full_width = F) %>%
row_spec(c(7:12, 19:24), background = "wheat")| n_traits | resid_method | method | L | converged |
|---|---|---|---|---|
| 5 | all | mnm_rss_shared | 2 | 1.000 |
| 5 | identity | mnm_rss_shared | 2 | 0.990 |
| 5 | null | mnm_rss_shared | 2 | 1.000 |
| 5 | oracle | mnm_rss_shared | 2 | 0.965 |
| 5 | flash | mnm_shared | 2 | 0.955 |
| 5 | oracle | mnm_shared | 2 | 0.930 |
| 5 | all | mnm_rss_shared | 10 | 0.955 |
| 5 | identity | mnm_rss_shared | 10 | 0.980 |
| 5 | null | mnm_rss_shared | 10 | 0.900 |
| 5 | oracle | mnm_rss_shared | 10 | 0.945 |
| 5 | flash | mnm_shared | 10 | 0.955 |
| 5 | oracle | mnm_shared | 10 | 0.930 |
| 10 | all | mnm_rss_shared | 2 | 0.990 |
| 10 | identity | mnm_rss_shared | 2 | 0.980 |
| 10 | null | mnm_rss_shared | 2 | 0.985 |
| 10 | oracle | mnm_rss_shared | 2 | 0.985 |
| 10 | flash | mnm_shared | 2 | 0.915 |
| 10 | oracle | mnm_shared | 2 | 0.905 |
| 10 | all | mnm_rss_shared | 10 | 0.945 |
| 10 | identity | mnm_rss_shared | 10 | 0.955 |
| 10 | null | mnm_rss_shared | 10 | 0.905 |
| 10 | oracle | mnm_rss_shared | 10 | 0.955 |
| 10 | flash | mnm_shared | 10 | 0.915 |
| 10 | oracle | mnm_shared | 10 | 0.905 |
purity = aggregate(purity~n_traits + resid_method + method + L, res.prior.oracle, mean)
purity = purity[order(purity$n_traits, purity$L),]
rownames(purity) = NULL
knitr::kable(purity) %>% kable_styling(full_width = F) %>%
row_spec(c(7:12, 19:24, 31:36), background = "wheat")| n_traits | resid_method | method | L | purity |
|---|---|---|---|---|
| 5 | all | mnm_rss_shared | 1 | 0.9403463 |
| 5 | identity | mnm_rss_shared | 1 | 0.9966379 |
| 5 | null | mnm_rss_shared | 1 | 0.9868357 |
| 5 | oracle | mnm_rss_shared | 1 | 0.9969791 |
| 5 | flash | mnm_shared | 1 | 0.9941027 |
| 5 | oracle | mnm_shared | 1 | 0.9965768 |
| 5 | all | mnm_rss_shared | 2 | 0.9923665 |
| 5 | identity | mnm_rss_shared | 2 | 0.9966379 |
| 5 | null | mnm_rss_shared | 2 | 0.9860790 |
| 5 | oracle | mnm_rss_shared | 2 | 0.9969791 |
| 5 | flash | mnm_shared | 2 | 0.9941027 |
| 5 | oracle | mnm_shared | 2 | 0.9965768 |
| 5 | all | mnm_rss_shared | 10 | 0.9999161 |
| 5 | identity | mnm_rss_shared | 10 | 0.9966379 |
| 5 | null | mnm_rss_shared | 10 | 0.9888716 |
| 5 | oracle | mnm_rss_shared | 10 | 0.9969791 |
| 5 | flash | mnm_shared | 10 | 0.9941027 |
| 5 | oracle | mnm_shared | 10 | 0.9965768 |
| 10 | all | mnm_rss_shared | 1 | 0.9394543 |
| 10 | identity | mnm_rss_shared | 1 | 0.9987209 |
| 10 | null | mnm_rss_shared | 1 | 0.9952346 |
| 10 | oracle | mnm_rss_shared | 1 | 0.9987721 |
| 10 | flash | mnm_shared | 1 | 0.9965968 |
| 10 | oracle | mnm_shared | 1 | 0.9986715 |
| 10 | all | mnm_rss_shared | 2 | 0.9978775 |
| 10 | identity | mnm_rss_shared | 2 | 0.9987209 |
| 10 | null | mnm_rss_shared | 2 | 0.9919765 |
| 10 | oracle | mnm_rss_shared | 2 | 0.9987721 |
| 10 | flash | mnm_shared | 2 | 0.9965968 |
| 10 | oracle | mnm_shared | 2 | 0.9986715 |
| 10 | all | mnm_rss_shared | 10 | 1.0000000 |
| 10 | identity | mnm_rss_shared | 10 | 0.9987209 |
| 10 | null | mnm_rss_shared | 10 | 0.9936072 |
| 10 | oracle | mnm_rss_shared | 10 | 0.9987721 |
| 10 | flash | mnm_shared | 10 | 0.9965968 |
| 10 | oracle | mnm_shared | 10 | 0.9986715 |
total_true_included = aggregate(total_true_included ~ n_traits + resid_method + method + L, res.prior.oracle, sum)
total_true = aggregate(total_true ~ n_traits + resid_method + method + L, res.prior.oracle, sum)
cs_overlap = aggregate(overlap_cs ~ n_traits + resid_method + method + L, res.prior.oracle, sum)
snp_overlap = aggregate(overlap_var ~ n_traits + resid_method + method + L, res.prior.oracle, sum)
power = merge(total_true_included, total_true, by = c( 'n_traits' , 'resid_method' , 'method' , 'L'))
power = merge(power, cs_overlap, by = c( 'n_traits' , 'resid_method' , 'method' , 'L'))
power = merge(power, snp_overlap, by = c( 'n_traits' , 'resid_method' , 'method' , 'L'))
power$power = round(power$total_true_included/power$total_true,3)
power$overlap_cs = round(power$overlap_cs, 3)
power$overlap_var = round(power$overlap_var, 3)
power = power[order(power$n_traits, power$L, power$method),]
rownames(power) = NULL
knitr::kable(power) %>% kable_styling(full_width = F) %>%
row_spec(c(7:12, 19:24, 31:36), background = "wheat")| n_traits | resid_method | method | L | total_true_included | total_true | overlap_cs | overlap_var | power |
|---|---|---|---|---|---|---|---|---|
| 5 | all | mnm_rss_shared | 1 | 39 | 200 | 0 | 0 | 0.195 |
| 5 | identity | mnm_rss_shared | 1 | 191 | 200 | 0 | 0 | 0.955 |
| 5 | null | mnm_rss_shared | 1 | 162 | 200 | 0 | 0 | 0.810 |
| 5 | oracle | mnm_rss_shared | 1 | 190 | 200 | 0 | 0 | 0.950 |
| 5 | flash | mnm_shared | 1 | 198 | 200 | 0 | 0 | 0.990 |
| 5 | oracle | mnm_shared | 1 | 195 | 200 | 0 | 0 | 0.975 |
| 5 | all | mnm_rss_shared | 2 | 41 | 200 | 0 | 0 | 0.205 |
| 5 | identity | mnm_rss_shared | 2 | 191 | 200 | 0 | 0 | 0.955 |
| 5 | null | mnm_rss_shared | 2 | 165 | 200 | 0 | 0 | 0.825 |
| 5 | oracle | mnm_rss_shared | 2 | 190 | 200 | 0 | 0 | 0.950 |
| 5 | flash | mnm_shared | 2 | 198 | 200 | 0 | 0 | 0.990 |
| 5 | oracle | mnm_shared | 2 | 195 | 200 | 0 | 0 | 0.975 |
| 5 | all | mnm_rss_shared | 10 | 58 | 200 | 0 | 0 | 0.290 |
| 5 | identity | mnm_rss_shared | 10 | 191 | 200 | 0 | 0 | 0.955 |
| 5 | null | mnm_rss_shared | 10 | 165 | 200 | 1 | 1 | 0.825 |
| 5 | oracle | mnm_rss_shared | 10 | 190 | 200 | 0 | 0 | 0.950 |
| 5 | flash | mnm_shared | 10 | 198 | 200 | 0 | 0 | 0.990 |
| 5 | oracle | mnm_shared | 10 | 195 | 200 | 0 | 0 | 0.975 |
| 10 | all | mnm_rss_shared | 1 | 38 | 200 | 0 | 0 | 0.190 |
| 10 | identity | mnm_rss_shared | 1 | 186 | 200 | 0 | 0 | 0.930 |
| 10 | null | mnm_rss_shared | 1 | 157 | 200 | 0 | 0 | 0.785 |
| 10 | oracle | mnm_rss_shared | 1 | 186 | 200 | 0 | 0 | 0.930 |
| 10 | flash | mnm_shared | 1 | 200 | 200 | 0 | 0 | 1.000 |
| 10 | oracle | mnm_shared | 1 | 198 | 200 | 0 | 0 | 0.990 |
| 10 | all | mnm_rss_shared | 2 | 43 | 200 | 0 | 0 | 0.215 |
| 10 | identity | mnm_rss_shared | 2 | 186 | 200 | 0 | 0 | 0.930 |
| 10 | null | mnm_rss_shared | 2 | 156 | 200 | 0 | 0 | 0.780 |
| 10 | oracle | mnm_rss_shared | 2 | 186 | 200 | 0 | 0 | 0.930 |
| 10 | flash | mnm_shared | 2 | 200 | 200 | 0 | 0 | 1.000 |
| 10 | oracle | mnm_shared | 2 | 198 | 200 | 0 | 0 | 0.990 |
| 10 | all | mnm_rss_shared | 10 | 46 | 200 | 0 | 0 | 0.230 |
| 10 | identity | mnm_rss_shared | 10 | 186 | 200 | 0 | 0 | 0.930 |
| 10 | null | mnm_rss_shared | 10 | 155 | 200 | 0 | 0 | 0.775 |
| 10 | oracle | mnm_rss_shared | 10 | 186 | 200 | 0 | 0 | 0.930 |
| 10 | flash | mnm_shared | 10 | 200 | 200 | 0 | 0 | 1.000 |
| 10 | oracle | mnm_shared | 10 | 198 | 200 | 0 | 0 | 0.990 |
valid = aggregate(valid ~ n_traits + resid_method + method + L, res.prior.oracle, sum)
total = aggregate(total ~ n_traits + resid_method + method + L, res.prior.oracle, sum)
fdr = merge(valid, total, by = c( 'n_traits' , 'resid_method' , 'method', 'L'))
fdr$fdr = round((fdr$total - fdr$valid)/fdr$total,3)
fdr = fdr[order(fdr$n_traits, fdr$L, fdr$method),]
rownames(fdr) = NULL
knitr::kable(fdr) %>% kable_styling(full_width = F) %>%
row_spec(c(7:12, 19:24, 31:36), background = "wheat")| n_traits | resid_method | method | L | valid | total | fdr |
|---|---|---|---|---|---|---|
| 5 | all | mnm_rss_shared | 1 | 39 | 191 | 0.796 |
| 5 | identity | mnm_rss_shared | 1 | 191 | 200 | 0.045 |
| 5 | null | mnm_rss_shared | 1 | 162 | 199 | 0.186 |
| 5 | oracle | mnm_rss_shared | 1 | 190 | 200 | 0.050 |
| 5 | flash | mnm_shared | 1 | 198 | 200 | 0.010 |
| 5 | oracle | mnm_shared | 1 | 195 | 200 | 0.025 |
| 5 | all | mnm_rss_shared | 2 | 41 | 382 | 0.893 |
| 5 | identity | mnm_rss_shared | 2 | 191 | 200 | 0.045 |
| 5 | null | mnm_rss_shared | 2 | 165 | 284 | 0.419 |
| 5 | oracle | mnm_rss_shared | 2 | 190 | 200 | 0.050 |
| 5 | flash | mnm_shared | 2 | 198 | 200 | 0.010 |
| 5 | oracle | mnm_shared | 2 | 195 | 200 | 0.025 |
| 5 | all | mnm_rss_shared | 10 | 58 | 1850 | 0.969 |
| 5 | identity | mnm_rss_shared | 10 | 191 | 200 | 0.045 |
| 5 | null | mnm_rss_shared | 10 | 165 | 544 | 0.697 |
| 5 | oracle | mnm_rss_shared | 10 | 190 | 200 | 0.050 |
| 5 | flash | mnm_shared | 10 | 198 | 200 | 0.010 |
| 5 | oracle | mnm_shared | 10 | 195 | 200 | 0.025 |
| 10 | all | mnm_rss_shared | 1 | 38 | 190 | 0.800 |
| 10 | identity | mnm_rss_shared | 1 | 186 | 200 | 0.070 |
| 10 | null | mnm_rss_shared | 1 | 157 | 200 | 0.215 |
| 10 | oracle | mnm_rss_shared | 1 | 186 | 200 | 0.070 |
| 10 | flash | mnm_shared | 1 | 200 | 200 | 0.000 |
| 10 | oracle | mnm_shared | 1 | 198 | 200 | 0.010 |
| 10 | all | mnm_rss_shared | 2 | 43 | 393 | 0.891 |
| 10 | identity | mnm_rss_shared | 2 | 186 | 200 | 0.070 |
| 10 | null | mnm_rss_shared | 2 | 156 | 296 | 0.473 |
| 10 | oracle | mnm_rss_shared | 2 | 186 | 200 | 0.070 |
| 10 | flash | mnm_shared | 2 | 200 | 200 | 0.000 |
| 10 | oracle | mnm_shared | 2 | 198 | 200 | 0.010 |
| 10 | all | mnm_rss_shared | 10 | 46 | 1929 | 0.976 |
| 10 | identity | mnm_rss_shared | 10 | 186 | 200 | 0.070 |
| 10 | null | mnm_rss_shared | 10 | 155 | 845 | 0.817 |
| 10 | oracle | mnm_rss_shared | 10 | 186 | 200 | 0.070 |
| 10 | flash | mnm_shared | 10 | 200 | 200 | 0.000 |
| 10 | oracle | mnm_shared | 10 | 198 | 200 | 0.010 |
elbo_converged = aggregate(converged~n_traits + resid_method + method + L, res.prior.oracle, mean)
elbo_converged = elbo_converged[which(elbo_converged$L!=1),]
elbo_converged = elbo_converged[order(elbo_converged$n_traits),]
rownames(elbo_converged) = NULL
knitr::kable(elbo_converged) %>% kable_styling(full_width = F) %>%
row_spec(c(7:12, 19:24), background = "wheat")| n_traits | resid_method | method | L | converged |
|---|---|---|---|---|
| 5 | all | mnm_rss_shared | 2 | 1.000 |
| 5 | identity | mnm_rss_shared | 2 | 0.990 |
| 5 | null | mnm_rss_shared | 2 | 0.990 |
| 5 | oracle | mnm_rss_shared | 2 | 0.975 |
| 5 | flash | mnm_shared | 2 | 0.955 |
| 5 | oracle | mnm_shared | 2 | 0.930 |
| 5 | all | mnm_rss_shared | 10 | 0.860 |
| 5 | identity | mnm_rss_shared | 10 | 0.990 |
| 5 | null | mnm_rss_shared | 10 | 0.895 |
| 5 | oracle | mnm_rss_shared | 10 | 0.975 |
| 5 | flash | mnm_shared | 10 | 0.955 |
| 5 | oracle | mnm_shared | 10 | 0.930 |
| 10 | all | mnm_rss_shared | 2 | 1.000 |
| 10 | identity | mnm_rss_shared | 2 | 0.980 |
| 10 | null | mnm_rss_shared | 2 | 0.985 |
| 10 | oracle | mnm_rss_shared | 2 | 0.980 |
| 10 | flash | mnm_shared | 2 | 0.915 |
| 10 | oracle | mnm_shared | 2 | 0.905 |
| 10 | all | mnm_rss_shared | 10 | 0.865 |
| 10 | identity | mnm_rss_shared | 10 | 0.980 |
| 10 | null | mnm_rss_shared | 10 | 0.870 |
| 10 | oracle | mnm_rss_shared | 10 | 0.980 |
| 10 | flash | mnm_shared | 10 | 0.915 |
| 10 | oracle | mnm_shared | 10 | 0.905 |
sessionInfo()R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)
Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] knitr_1.20 kableExtra_1.1.0 dplyr_0.8.0.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.3 highr_0.7 pillar_1.4.3
[4] compiler_3.5.1 later_0.7.5 git2r_0.26.1
[7] workflowr_1.6.0 tools_3.5.1 digest_0.6.25
[10] viridisLite_0.3.0 evaluate_0.12 tibble_2.1.3
[13] lifecycle_0.1.0 pkgconfig_2.0.3 rlang_0.4.4
[16] rstudioapi_0.10 yaml_2.2.0 stringr_1.4.0
[19] httr_1.3.1 xml2_1.2.0 fs_1.3.1
[22] vctrs_0.2.3 hms_0.5.3 webshot_0.5.1
[25] rprojroot_1.3-2 tidyselect_0.2.5 glue_1.3.1
[28] R6_2.4.1 rmarkdown_1.10 purrr_0.3.2
[31] readr_1.3.1 magrittr_1.5 whisker_0.3-2
[34] backports_1.1.5 scales_1.1.0 promises_1.0.1
[37] htmltools_0.3.6 assertthat_0.2.1 rvest_0.3.2
[40] colorspace_1.4-1 httpuv_1.4.5 stringi_1.4.3
[43] munsell_0.5.0 crayon_1.3.4