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<h1 class="title toc-ignore">GTEx V6</h1>
<h4 class="author"><em>Yuxin Zou</em></h4>
<h4 class="date"><em>2018-12-20</em></h4>
</div>
<p><strong>Last updated:</strong> 2019-01-01</p>
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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. <br><br> 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 <code>wflow_publish</code> or <code>wflow_git_commit</code>). 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:
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<hr />
<pre class="r"><code>library(flashr)
library(mixsqp)
library(mashr)</code></pre>
<pre><code>Loading required package: ashr</code></pre>
<pre class="r"><code>library(knitr)
library(kableExtra)
library(ggplot2)
library(gridExtra)</code></pre>
<pre class="r"><code>gtex <- readRDS(gzcon(url("https://github.com/stephenslab/gtexresults/blob/master/data/MatrixEQTLSumStats.Portable.Z.rds?raw=TRUE")))</code></pre>
<pre class="r"><code>strong.z = gtex$strong.z
data.strong = mash_set_data(strong.z)
data.random = mash_set_data(gtex$random.b, gtex$random.s)</code></pre>
<div id="data-driven-covariances" class="section level2">
<h2>Data Driven Covariances</h2>
<p>Flash:</p>
<pre class="r"><code>my_init_fn <- function(Y, K = 1) {
ret = flashr:::udv_si(Y, K)
pos_sum = sum(ret$v[ret$v > 0])
neg_sum = -sum(ret$v[ret$v < 0])
if (neg_sum > pos_sum) {
return(list(u = -ret$u, d = ret$d, v = -ret$v))
} else
return(ret)
}
flash_pipeline = function(data, ...) {
## current state-of-the art
## suggested by Jason Willwerscheid
## cf: discussion section of
## https://willwerscheid.github.io/MASHvFLASH/MASHvFLASHnn2.html
ebnm_fn = "ebnm_ash"
ebnm_param = list(l = list(mixcompdist = "normal",
optmethod = "mixSQP"),
f = list(mixcompdist = "+uniform",
optmethod = "mixSQP"))
##
fl_g <- flashr:::flash_greedy_workhorse(data,
var_type = "constant",
ebnm_fn = ebnm_fn,
ebnm_param = ebnm_param,
init_fn = "my_init_fn",
stopping_rule = "factors",
tol = 1e-3,
verbose_output = "odF")
fl_b <- flashr:::flash_backfit_workhorse(data,
f_init = fl_g,
var_type = "constant",
ebnm_fn = ebnm_fn,
ebnm_param = ebnm_param,
stopping_rule = "factors",
tol = 1e-3,
verbose_output = "odF")
return(fl_b)
}
cov_flash = function(data, subset = NULL, non_canonical = FALSE, save_model = NULL) {
if(is.null(subset)) subset = 1:mashr:::n_effects(data)
b.center = apply(data$Bhat, 2, function(x) x - mean(x))
## Only keep factors with at least two values greater than 1 / sqrt(n)
find_nonunique_effects <- function(fl) {
thresh <- 1/sqrt(ncol(fl$fitted_values))
vals_above_avg <- colSums(fl$ldf$f > thresh)
nonuniq_effects <- which(vals_above_avg > 1)
return(fl$ldf$f[, nonuniq_effects, drop = FALSE])
}
fmodel = flash_pipeline(b.center)
if (non_canonical)
flash_f = find_nonunique_effects(fmodel)
else
flash_f = fmodel$ldf$f
## row.names(flash_f) = colnames(b)
if (!is.null(save_model)) saveRDS(list(model=fmodel, factors=flash_f), save_model)
if(ncol(flash_f) == 0){
U.flash = list("tFLASH" = t(fmodel$fitted_values) %*% fmodel$fitted_values / nrow(fmodel$fitted_values))
} else{
U.flash = c(cov_from_factors(t(as.matrix(flash_f)), "FLASH"),
list("tFLASH" = t(fmodel$fitted_values) %*% fmodel$fitted_values / nrow(fmodel$fitted_values)))
}
return(U.flash)
}</code></pre>
<pre class="r"><code>U.f = cov_flash(data.strong, non_canonical = TRUE, save_model = 'output/GTExV6/flash_model.rds')
saveRDS(U.f, 'output/GTExV6/flash_cov.rds')</code></pre>
<pre class="r"><code>missing.tissues <- c(7, 8, 19, 20, 24, 25, 31, 34, 37)
gtex.colors <- read.table("https://github.com/stephenslab/gtexresults/blob/master/data/GTExColors.txt?raw=TRUE", sep = '\t', comment.char = '')[-missing.tissues, 2]
gtex.colors <- as.character(gtex.colors)
fl_model = readRDS('output/GTExV6/flash_model.rds')$model
factors = readRDS('output/GTExV6/flash_model.rds')$factors
par(mfrow = c(2, 3))
for(k in 1:16){
barplot(factors[,k], col=gtex.colors, names.arg = FALSE, axes = FALSE, main=paste0("Factor ", k))
}</code></pre>
<p><img src="figure/GTExV6.Rmd/flash%20factors%20plot-1.png" width="672" style="display: block; margin: auto;" /></p>
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<pre class="r"><code>fll_model = flash_pipeline(fl_model$ldf$l)
saveRDS(fll_model, 'output/GTExV6/flash_loading_model.rds')</code></pre>
<pre class="r"><code>U.pca = cov_pca(data.strong, 5)</code></pre>
<pre class="r"><code>U.ed = cov_ed(data.strong, c(U.f, U.pca))</code></pre>
<pre class="r"><code>U.ed = readRDS('output/GTExV6/Ued.rds')</code></pre>
<pre class="r"><code>U.c = cov_canonical(data.random)</code></pre>
<pre class="r"><code>data.strong = mash_set_data(Bhat = gtex$strong.b, Shat = gtex$strong.s)</code></pre>
<pre class="r"><code>m.ignore = mash(data.random, c(U.c, U.ed), outputlevel = 1)
m.ignore$result = mash_compute_posterior_matrices(m.ignore, data.strong)</code></pre>
<pre class="r"><code>V.simple = estimate_null_correlation_simple(data.random)</code></pre>
<pre class="r"><code>data.random.V.simple = mash_update_data(data.random, V = V.simple)
m.simple = mash(data.random.V.simple, c(U.c, U.ed), outputlevel = 1)
data.strong.V.simple = mash_update_data(data.strong, V = V.simple)
m.simple$result = mash_compute_posterior_matrices(m.simple, data.strong.V.simple)</code></pre>
<pre class="r"><code>set.seed(1)
random.subset = sample(1:nrow(gtex$random.b),5000)
data.random.s = mash_set_data(gtex$random.b[random.subset,], gtex$random.s[random.subset,])
current = estimate_null_correlation(data.random.s, c(U.c, U.ed), max_iter = 6)
V.current = current$V
data.random.V.current = mash_update_data(data.random, V = V.current)
m.current = mash(data.random.V.current, c(U.c, U.ed), outputlevel = 1)
data.strong = mash_update_data(data.strong, V = V.current)
m.current$result = mash_compute_posterior_matrices(m.current, data.strong)</code></pre>
<pre class="r"><code>V = get(load('~/Documents/GitHub/GTEx/data/genewide_ash_out_tissue_mat_halfuniform_non_mode.rda'))
# select tissue
tissue_labels <- read.table(file = "~/Documents/GitHub/GTEx/data/samples_id.txt")[,3]
U <- unique(tissue_labels)
tissues = c(1:6, 9:18, 21:23,26:30,32:33,35:36,38:53)
V = V[tissues,tissues,]
V.strong = V
for(i in 1:nrow(gtex$strong.b)){
V.strong[,,i] = as.matrix(Matrix::nearPD(V[,,i], conv.tol=1.e-05, corr = TRUE, maxit = 200, doSym = TRUE)$mat)
}
saveRDS(V.strong, 'output/GTExV6/V_strong_genewide.rds')
# select genes
gene_names <- as.character(read.table(file = "~/Documents/GitHub/GTEx/data/gene_names_GTEX_V6.txt")[,1])
gene_names_1 <- as.character(sapply(gene_names, function(x) return(strsplit(x, "[.]")[[1]][1])))
data.random.names = rownames(data.random$Bhat)
data.random.names.1 = as.character(sapply(data.random.names, function(x) return(strsplit(x, "[.]")[[1]][1])))
V.random = array(NA, dim = c(44,44,nrow(gtex$random.b)))
for(i in 1:nrow(gtex$random.b)){
numg <- grep(data.random.names.1[i], gene_names_1)
V.random[,,i] = as.matrix(Matrix::nearPD(V[,,numg], conv.tol=1.e-05, corr = TRUE, doSym = TRUE)$mat)
}
saveRDS(V.random, 'output/GTExV6/V_random_genewide.rds')
data.random.V3 = mash_update_data(data.random, V = V.random)
m.V3 = mash(data.random.V3, c(U.c, U.ed), outputlevel = 1, algorithm.version = 'R')
data.strong.V3 = mash_update_data(data.strong, V = V.strong)
m.V3$result = mash_compute_posterior_matrices(m.V3, data.strong.V3, algorithm.version = 'R')</code></pre>
<pre class="r"><code># read model
m_ignore = readRDS('output/GTExV6/m_ignore_post.rds')
m_ignore_EZ = readRDS('output/GTExV6/m_ignore_EZ_post.rds')
m_simple = readRDS('output/GTExV6/m_simple_post.rds')
m_simple_EZ = readRDS('output/GTExV6/m_simple_EZ_post.rds')
m_current = readRDS('output/GTExV6/m_current_post.rds')
m_current_EZ = readRDS('output/GTExV6/m_current_EZ_post.rds')
m_V3 = readRDS('output/GTExV6/m_V3_genewide_post.rds')
m_V3_EZ = readRDS('output/GTExV6/m_V3_genewide_EZ_post.rds')</code></pre>
<pre class="r"><code># pdf('../output/GTExV6/Figures/SimpleV.pdf')
corrplot::corrplot(V.simple, method='color', type='upper', tl.col="black", tl.srt=45, tl.cex = 0.5, diag = FALSE, col=colorRampPalette(c("blue", "white", "red"))(200), cl.lim = c(-1,1), title = 'Simple', mar=c(0,0,5,0))</code></pre>
<p><img src="figure/GTExV6.Rmd/V-1.png" width="768" style="display: block; margin: auto;" /></p>
<details> <summary><em>Expand here to see past versions of V-1.png:</em></summary>
<table style="border-collapse:separate; border-spacing:5px;">
<thead>
<tr>
<th style="text-align:left;">
Version
</th>
<th style="text-align:left;">
Author
</th>
<th style="text-align:left;">
Date
</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;">
<a href="https://github.com/zouyuxin/GTEx/blob/5306c8f76093dc136121d237eec1dfd5693cec79/docs/figure/GTExV6.Rmd/V-1.png" target="_blank">5306c8f</a>
</td>
<td style="text-align:left;">
zouyuxin
</td>
<td style="text-align:left;">
2019-01-01
</td>
</tr>
<tr>
<td style="text-align:left;">
<a href="https://github.com/zouyuxin/GTEx/blob/a4437cb53fa9d56504bb2e8176c79f28914b1b17/docs/figure/GTExV6.Rmd/V-1.png" target="_blank">a4437cb</a>
</td>
<td style="text-align:left;">
zouyuxin
</td>
<td style="text-align:left;">
2019-01-01
</td>
</tr>
</tbody>
</table>
<p></details></p>
<pre class="r"><code># dev.off()
V.current = readRDS('output/GTExV6/currentV_EZ.rds')
V.current = V.current$V
# pdf('../output/GTExV6/Figures/CurrentEZV.pdf')
corrplot::corrplot(V.current, method='color', type='upper', tl.col="black", tl.srt=45, tl.cex = 0.5, diag = FALSE, col=colorRampPalette(c("blue", "white", "red"))(200), cl.lim = c(-1,1), title = 'Current EZ', mar=c(0,0,5,0))</code></pre>
<p><img src="figure/GTExV6.Rmd/V-2.png" width="768" style="display: block; margin: auto;" /></p>
<details> <summary><em>Expand here to see past versions of V-2.png:</em></summary>
<table style="border-collapse:separate; border-spacing:5px;">
<thead>
<tr>
<th style="text-align:left;">
Version
</th>
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Author
</th>
<th style="text-align:left;">
Date
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</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;">
<a href="https://github.com/zouyuxin/GTEx/blob/5306c8f76093dc136121d237eec1dfd5693cec79/docs/figure/GTExV6.Rmd/V-2.png" target="_blank">5306c8f</a>
</td>
<td style="text-align:left;">
zouyuxin
</td>
<td style="text-align:left;">
2019-01-01
</td>
</tr>
</tbody>
</table>
<p></details></p>
<pre class="r"><code># dev.off()</code></pre>
<pre class="r"><code>logliks = c(get_loglik(m_ignore), get_loglik(m_simple), get_loglik(m_current), get_loglik(m_V3))
logliks_EZ = c(get_loglik(m_ignore_EZ), get_loglik(m_simple_EZ), get_loglik(m_current_EZ), get_loglik(m_V3_EZ))
tmp = cbind(logliks, logliks_EZ)
row.names(tmp) = c('Ignore', 'Simple', 'Current', 'V3')
colnames(tmp) = c('EE', 'EZ')
tmp %>% kable() %>% kable_styling()</code></pre>
<table class="table" style="margin-left: auto; margin-right: auto;">
<thead>
<tr>
<th style="text-align:left;">
</th>
<th style="text-align:right;">
EE
</th>
<th style="text-align:right;">
EZ
</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;">
Ignore
</td>
<td style="text-align:right;">
929188.2
</td>
<td style="text-align:right;">
935288.4
</td>
</tr>
<tr>
<td style="text-align:left;">
Simple
</td>
<td style="text-align:right;">
933359.2
</td>
<td style="text-align:right;">
936783.2
</td>
</tr>
<tr>
<td style="text-align:left;">
Current
</td>
<td style="text-align:right;">
937323.7
</td>
<td style="text-align:right;">
939685.2
</td>
</tr>
<tr>
<td style="text-align:left;">
V3
</td>
<td style="text-align:right;">
860927.1
</td>
<td style="text-align:right;">
897029.6
</td>
</tr>
</tbody>
</table>
<pre class="r"><code>par(mfrow=c(1,2))
barplot(get_estimated_pi(m_ignore), las=2, cex.names = 0.7, main = 'Ignore EE')
barplot(get_estimated_pi(m_simple), las=2, cex.names = 0.7, main = 'Simple EE')</code></pre>
<p><img src="figure/GTExV6.Rmd/plot%20weights-1.png" width="1920" style="display: block; margin: auto;" /></p>
<details> <summary><em>Expand here to see past versions of plot weights-1.png:</em></summary>
<table style="border-collapse:separate; border-spacing:5px;">
<thead>
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<th style="text-align:left;">
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Author
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<th style="text-align:left;">
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<td style="text-align:left;">
<a href="https://github.com/zouyuxin/GTEx/blob/5306c8f76093dc136121d237eec1dfd5693cec79/docs/figure/GTExV6.Rmd/plot weights-1.png" target="_blank">5306c8f</a>
</td>
<td style="text-align:left;">
zouyuxin
</td>
<td style="text-align:left;">
2019-01-01
</td>
</tr>
<tr>
<td style="text-align:left;">
<a href="https://github.com/zouyuxin/GTEx/blob/a4437cb53fa9d56504bb2e8176c79f28914b1b17/docs/figure/GTExV6.Rmd/plot weights-1.png" target="_blank">a4437cb</a>
</td>
<td style="text-align:left;">
zouyuxin
</td>
<td style="text-align:left;">
2019-01-01
</td>
</tr>
</tbody>
</table>
<p></details></p>
<pre class="r"><code>barplot(get_estimated_pi(m_current), las=2, cex.names = 0.7, main = 'Current EE')
barplot(get_estimated_pi(m_V3), las=2, cex.names = 0.7, main = 'V3 EE')</code></pre>
<p><img src="figure/GTExV6.Rmd/plot%20weights-2.png" width="1920" style="display: block; margin: auto;" /></p>
<details> <summary><em>Expand here to see past versions of plot weights-2.png:</em></summary>
<table style="border-collapse:separate; border-spacing:5px;">
<thead>
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<td style="text-align:left;">
<a href="https://github.com/zouyuxin/GTEx/blob/5306c8f76093dc136121d237eec1dfd5693cec79/docs/figure/GTExV6.Rmd/plot weights-2.png" target="_blank">5306c8f</a>
</td>
<td style="text-align:left;">
zouyuxin
</td>
<td style="text-align:left;">
2019-01-01
</td>
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<td style="text-align:left;">
<a href="https://github.com/zouyuxin/GTEx/blob/a4437cb53fa9d56504bb2e8176c79f28914b1b17/docs/figure/GTExV6.Rmd/plot weights-2.png" target="_blank">a4437cb</a>
</td>
<td style="text-align:left;">
zouyuxin
</td>
<td style="text-align:left;">
2019-01-01
</td>
</tr>
</tbody>
</table>
<p></details></p>
<pre class="r"><code>barplot(get_estimated_pi(m_ignore_EZ), las=2, cex.names = 0.7, main = 'Ignore EZ')
barplot(get_estimated_pi(m_simple_EZ), las=2, cex.names = 0.7, main = 'Simple EZ')</code></pre>
<p><img src="figure/GTExV6.Rmd/plot%20weights-3.png" width="1920" style="display: block; margin: auto;" /></p>
<details> <summary><em>Expand here to see past versions of plot weights-3.png:</em></summary>
<table style="border-collapse:separate; border-spacing:5px;">
<thead>
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<th style="text-align:left;">
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</thead>
<tbody>
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<td style="text-align:left;">
<a href="https://github.com/zouyuxin/GTEx/blob/5306c8f76093dc136121d237eec1dfd5693cec79/docs/figure/GTExV6.Rmd/plot weights-3.png" target="_blank">5306c8f</a>
</td>
<td style="text-align:left;">
zouyuxin
</td>
<td style="text-align:left;">
2019-01-01
</td>
</tr>
<tr>
<td style="text-align:left;">
<a href="https://github.com/zouyuxin/GTEx/blob/a4437cb53fa9d56504bb2e8176c79f28914b1b17/docs/figure/GTExV6.Rmd/plot weights-3.png" target="_blank">a4437cb</a>
</td>
<td style="text-align:left;">
zouyuxin
</td>
<td style="text-align:left;">
2019-01-01
</td>
</tr>
</tbody>
</table>
<p></details></p>
<pre class="r"><code>barplot(get_estimated_pi(m_current_EZ), las=2, cex.names = 0.7, main = 'Current EZ')
barplot(get_estimated_pi(m_V3_EZ), las=2, cex.names = 0.7, main = 'V3 EZ')</code></pre>
<p><img src="figure/GTExV6.Rmd/plot%20weights-4.png" width="1920" style="display: block; margin: auto;" /></p>
<details> <summary><em>Expand here to see past versions of plot weights-4.png:</em></summary>
<table style="border-collapse:separate; border-spacing:5px;">
<thead>
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<th style="text-align:left;">
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<th style="text-align:left;">
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<td style="text-align:left;">
<a href="https://github.com/zouyuxin/GTEx/blob/5306c8f76093dc136121d237eec1dfd5693cec79/docs/figure/GTExV6.Rmd/plot weights-4.png" target="_blank">5306c8f</a>
</td>
<td style="text-align:left;">
zouyuxin
</td>
<td style="text-align:left;">
2019-01-01
</td>
</tr>
<tr>
<td style="text-align:left;">
<a href="https://github.com/zouyuxin/GTEx/blob/a4437cb53fa9d56504bb2e8176c79f28914b1b17/docs/figure/GTExV6.Rmd/plot weights-4.png" target="_blank">a4437cb</a>
</td>
<td style="text-align:left;">
zouyuxin
</td>
<td style="text-align:left;">
2019-01-01
</td>
</tr>
</tbody>
</table>
<p></details></p>
<p>Number of significant:</p>
<pre class="r"><code>numsig_EE = c(length(get_significant_results(m_ignore)),
length(get_significant_results(m_simple)),
length(get_significant_results(m_current)),
length(get_significant_results(m_V3)))
numsig_EZ = c(length(get_significant_results(m_ignore_EZ)),
length(get_significant_results(m_simple_EZ)),
length(get_significant_results(m_current_EZ)),
length(get_significant_results(m_V3_EZ)))
tmp = cbind(numsig_EE, numsig_EZ)
row.names(tmp) = c('Ignore', 'Simple', 'Current', 'V3')
colnames(tmp) = c('EE', 'EZ')
tmp %>% kable() %>% kable_styling()</code></pre>
<table class="table" style="margin-left: auto; margin-right: auto;">
<thead>
<tr>
<th style="text-align:left;">
</th>
<th style="text-align:right;">
EE
</th>
<th style="text-align:right;">
EZ
</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;">
Ignore
</td>
<td style="text-align:right;">
14017
</td>
<td style="text-align:right;">
14221
</td>
</tr>
<tr>
<td style="text-align:left;">
Simple
</td>
<td style="text-align:right;">
13037
</td>
<td style="text-align:right;">
13485
</td>
</tr>
<tr>
<td style="text-align:left;">
Current
</td>
<td style="text-align:right;">
12803
</td>
<td style="text-align:right;">
13006
</td>
</tr>
<tr>
<td style="text-align:left;">
V3
</td>
<td style="text-align:right;">
16054
</td>
<td style="text-align:right;">
16069
</td>
</tr>
</tbody>
</table>
<p>The V3 model has more significant findings, which includes all significant findings in the other three models.</p>
<pre class="r"><code>length(intersect(get_significant_results(m_V3_EZ), get_significant_results(m_current_EZ)))</code></pre>
<pre><code>[1] 13006</code></pre>
<pre class="r"><code>length(intersect(get_significant_results(m_V3_EZ), get_significant_results(m_simple_EZ)))</code></pre>
<pre><code>[1] 13485</code></pre>
<pre class="r"><code>length(intersect(get_significant_results(m_V3_EZ), get_significant_results(m_ignore_EZ)))</code></pre>
<pre><code>[1] 14221</code></pre>
<p>The gene significant in <code>simple EZ</code>, not in <code>current EZ</code>:</p>
<pre class="r"><code>stronggene = data.frame(gtex$strong.b[5034,])
colnames(stronggene) = 'EffectSize'
stronggene$Group = row.names(stronggene)
stronggene$se = gtex$strong.s[5034,]
p1 = ggplot(stronggene, aes(y = EffectSize, x = Group)) +
geom_point(show.legend = FALSE, color=gtex.colors) + coord_flip() + ggtitle('ENSG00000135315') + ylim(c(-0.7,1)) + geom_errorbar(aes(ymin=EffectSize-1.96*se, ymax=EffectSize+1.96*se), width=0.4, show.legend = FALSE, color=gtex.colors) +
theme_bw(base_size=12) + theme(axis.text.y = element_text(colour = gtex.colors, size = 6))
stronggeneSimple = data.frame(m_simple_EZ$result$PosteriorMean[5034,])
colnames(stronggeneSimple) = 'EffectSize'
stronggeneSimple$Group = row.names(stronggeneSimple)
stronggeneSimple$se = m_simple_EZ$result$PosteriorSD[5034,]
p2 = ggplot(stronggeneSimple, aes(y = EffectSize, x = Group)) +
geom_point(show.legend = FALSE, color=gtex.colors) + coord_flip() + ggtitle('ENSG00000135315 Simple') + ylim(c(-0.7,1)) +
geom_errorbar(aes(ymin=EffectSize-1.96*se, ymax=EffectSize+1.96*se), width=0.4, show.legend = FALSE, color=gtex.colors) +
theme_bw(base_size=12) + theme(axis.text.y = element_text(colour = gtex.colors, size = 6))
stronggeneCurrent = data.frame(m_current_EZ$result$PosteriorMean[5034,])
colnames(stronggeneCurrent) = 'EffectSize'
stronggeneCurrent$Group = row.names(stronggeneCurrent)
stronggeneCurrent$se = m_current_EZ$result$PosteriorSD[5034,]
p3 = ggplot(stronggeneCurrent, aes(y = EffectSize, x = Group)) +
geom_point(show.legend = FALSE, color=gtex.colors) + ylim(c(-0.7,1)) + coord_flip() + ggtitle('ENSG00000135315 Current') +
geom_errorbar(aes(ymin=EffectSize-1.96*se, ymax=EffectSize+1.96*se), width=0.4, show.legend = FALSE, color=gtex.colors) +
theme_bw(base_size=12) + theme(axis.text.y = element_text(colour = gtex.colors, size = 6))
stronggeneV3 = data.frame(m_V3_EZ$result$PosteriorMean[5034,])
colnames(stronggeneV3) = 'EffectSize'
stronggeneV3$Group = row.names(stronggeneV3)
stronggeneV3$se = m_V3_EZ$result$PosteriorSD[5034,]
p4 = ggplot(stronggeneV3, aes(y = EffectSize, x = Group)) +
geom_point(show.legend = FALSE, color=gtex.colors) + ylim(c(-0.7,1)) + coord_flip() + ggtitle('ENSG00000135315 V3') +
geom_errorbar(aes(ymin=EffectSize-1.96*se, ymax=EffectSize+1.96*se), width=0.4, show.legend = FALSE, color=gtex.colors) +
theme_bw(base_size=12) + theme(axis.text.y = element_text(colour = gtex.colors, size = 6))
grid.arrange(p1, p2, p3, p4, nrow = 2)</code></pre>
<p><img src="figure/GTExV6.Rmd/unnamed-chunk-15-1.png" width="1440" style="display: block; margin: auto;" /></p>
<details> <summary><em>Expand here to see past versions of unnamed-chunk-15-1.png:</em></summary>
<table style="border-collapse:separate; border-spacing:5px;">
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<td style="text-align:left;">
<a href="https://github.com/zouyuxin/GTEx/blob/5306c8f76093dc136121d237eec1dfd5693cec79/docs/figure/GTExV6.Rmd/unnamed-chunk-15-1.png" target="_blank">5306c8f</a>
</td>
<td style="text-align:left;">
zouyuxin
</td>
<td style="text-align:left;">
2019-01-01
</td>
</tr>
<tr>
<td style="text-align:left;">
<a href="https://github.com/zouyuxin/GTEx/blob/a4437cb53fa9d56504bb2e8176c79f28914b1b17/docs/figure/GTExV6.Rmd/unnamed-chunk-15-1.png" target="_blank">a4437cb</a>
</td>
<td style="text-align:left;">
zouyuxin
</td>
<td style="text-align:left;">
2019-01-01
</td>
</tr>
</tbody>
</table>
<p></details></p>
<p>The gene <code>MCPH1</code>:</p>
<pre class="r"><code>stronggene = data.frame(gtex$strong.b[13837,])
colnames(stronggene) = 'EffectSize'
stronggene$Group = row.names(stronggene)
stronggene$se = gtex$strong.s[13837,]
p1 = ggplot(stronggene, aes(y = EffectSize, x = Group)) +
geom_point(show.legend = FALSE, color=gtex.colors) + coord_flip() + ggtitle('ENSG00000249898') + ylim(c(-1.3,1.1)) + geom_errorbar(aes(ymin=EffectSize-1.96*se, ymax=EffectSize+1.96*se), width=0.4, show.legend = FALSE, color=gtex.colors) +
theme_bw(base_size=12) + theme(axis.text.y = element_text(colour = gtex.colors, size = 6))
stronggeneCurrent = data.frame(m_current_EZ$result$PosteriorMean[13837,])
colnames(stronggeneCurrent) = 'EffectSize'
stronggeneCurrent$Group = row.names(stronggeneCurrent)
stronggeneCurrent$se = m_current_EZ$result$PosteriorSD[13837,]
p2 = ggplot(stronggeneCurrent, aes(y = EffectSize, x = Group)) +
geom_point(show.legend = FALSE, color=gtex.colors) + coord_flip() + ggtitle('ENSG00000249898 Current') + ylim(c(-1.3,1.1)) +
geom_errorbar(aes(ymin=EffectSize-1.96*se, ymax=EffectSize+1.96*se), width=0.4, show.legend = FALSE, color=gtex.colors) +
theme_bw(base_size=12) + theme(axis.text.y = element_text(colour = gtex.colors, size = 6))
stronggeneV3 = data.frame(m_V3_EZ$result$PosteriorMean[13837,])
colnames(stronggeneV3) = 'EffectSize'
stronggeneV3$Group = row.names(stronggeneV3)
stronggeneV3$se = m_V3_EZ$result$PosteriorSD[13837,]
p3 = ggplot(stronggeneV3, aes(y = EffectSize, x = Group)) +
geom_point(show.legend = FALSE, color=gtex.colors) + ylim(c(-1.3,1.1)) + coord_flip() + ggtitle('ENSG00000249898 V3') +
geom_errorbar(aes(ymin=EffectSize-1.96*se, ymax=EffectSize+1.96*se), width=0.4, show.legend = FALSE, color=gtex.colors) +
theme_bw(base_size=12) + theme(axis.text.y = element_text(colour = gtex.colors, size = 6))
grid.arrange(p1, p2, p3, nrow = 1)</code></pre>
<p><img src="figure/GTExV6.Rmd/unnamed-chunk-16-1.png" width="1920" style="display: block; margin: auto;" /></p>
<details> <summary><em>Expand here to see past versions of unnamed-chunk-16-1.png:</em></summary>
<table style="border-collapse:separate; border-spacing:5px;">
<thead>
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<th style="text-align:left;">
Version
</th>
<th style="text-align:left;">
Author
</th>
<th style="text-align:left;">
Date
</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;">
<a href="https://github.com/zouyuxin/GTEx/blob/5306c8f76093dc136121d237eec1dfd5693cec79/docs/figure/GTExV6.Rmd/unnamed-chunk-16-1.png" target="_blank">5306c8f</a>
</td>
<td style="text-align:left;">
zouyuxin
</td>
<td style="text-align:left;">
2019-01-01
</td>
</tr>
<tr>
<td style="text-align:left;">
<a href="https://github.com/zouyuxin/GTEx/blob/a4437cb53fa9d56504bb2e8176c79f28914b1b17/docs/figure/GTExV6.Rmd/unnamed-chunk-16-1.png" target="_blank">a4437cb</a>
</td>
<td style="text-align:left;">
zouyuxin
</td>
<td style="text-align:left;">
2019-01-01
</td>
</tr>
</tbody>
</table>
<p></details></p>
<p>The gene significant in <code>V3 EZ</code>, not in <code>current EZ</code>:</p>
<pre class="r"><code>ind = setdiff(get_significant_results(m_V3_EZ), get_significant_results(m_current_EZ))[1]
stronggene = data.frame(gtex$strong.b[ind,])
colnames(stronggene) = 'EffectSize'
stronggene$Group = row.names(stronggene)
stronggene$se = gtex$strong.s[ind,]
p1 = ggplot(stronggene, aes(y = EffectSize, x = Group)) +
geom_point(show.legend = FALSE, color=gtex.colors) + coord_flip() + ggtitle('ENSG00000126243') + ylim(c(-1.3,1.1)) + geom_errorbar(aes(ymin=EffectSize-1.96*se, ymax=EffectSize+1.96*se), width=0.4, show.legend = FALSE, color=gtex.colors) +
theme_bw(base_size=12) + theme(axis.text.y = element_text(colour = gtex.colors, size = 6))
stronggeneCurrent = data.frame(m_current_EZ$result$PosteriorMean[ind,])
colnames(stronggeneCurrent) = 'EffectSize'
stronggeneCurrent$Group = row.names(stronggeneCurrent)
stronggeneCurrent$se = m_current_EZ$result$PosteriorSD[ind,]
p2 = ggplot(stronggeneCurrent, aes(y = EffectSize, x = Group)) +
geom_point(show.legend = FALSE, color=gtex.colors) + coord_flip() + ggtitle('ENSG00000126243 Current') + ylim(c(-1.3,1.1)) +
geom_errorbar(aes(ymin=EffectSize-1.96*se, ymax=EffectSize+1.96*se), width=0.4, show.legend = FALSE, color=gtex.colors) +
theme_bw(base_size=12) + theme(axis.text.y = element_text(colour = gtex.colors, size = 6))
stronggeneV3 = data.frame(m_V3_EZ$result$PosteriorMean[ind,])
colnames(stronggeneV3) = 'EffectSize'
stronggeneV3$Group = row.names(stronggeneV3)
stronggeneV3$se = m_V3_EZ$result$PosteriorSD[ind,]
p3 = ggplot(stronggeneV3, aes(y = EffectSize, x = Group)) +
geom_point(show.legend = FALSE, color=gtex.colors) + ylim(c(-1.3,1.1)) + coord_flip() + ggtitle('ENSG00000126243 V3') +
geom_errorbar(aes(ymin=EffectSize-1.96*se, ymax=EffectSize+1.96*se), width=0.4, show.legend = FALSE, color=gtex.colors) +
theme_bw(base_size=12) + theme(axis.text.y = element_text(colour = gtex.colors, size = 6))
grid.arrange(p1, p2, p3, nrow = 1)</code></pre>
<p><img src="figure/GTExV6.Rmd/unnamed-chunk-17-1.png" width="1920" style="display: block; margin: auto;" /></p>
<details> <summary><em>Expand here to see past versions of unnamed-chunk-17-1.png:</em></summary>
<table style="border-collapse:separate; border-spacing:5px;">
<thead>
<tr>
<th style="text-align:left;">
Version
</th>
<th style="text-align:left;">
Author
</th>
<th style="text-align:left;">
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</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;">
<a href="https://github.com/zouyuxin/GTEx/blob/5306c8f76093dc136121d237eec1dfd5693cec79/docs/figure/GTExV6.Rmd/unnamed-chunk-17-1.png" target="_blank">5306c8f</a>
</td>
<td style="text-align:left;">
zouyuxin
</td>
<td style="text-align:left;">
2019-01-01
</td>
</tr>
<tr>
<td style="text-align:left;">
<a href="https://github.com/zouyuxin/GTEx/blob/a4437cb53fa9d56504bb2e8176c79f28914b1b17/docs/figure/GTExV6.Rmd/unnamed-chunk-17-1.png" target="_blank">a4437cb</a>
</td>
<td style="text-align:left;">
zouyuxin
</td>
<td style="text-align:left;">
2019-01-01
</td>
</tr>
</tbody>
</table>
<p></details></p>
<p>The pairwise sharing by magnitude</p>
<pre class="r"><code>par(mfrow = c(1,2))
x <- get_pairwise_sharing(m_ignore_EZ)
colnames(x) <- colnames(get_lfsr(m_ignore_EZ))
rownames(x) <- colnames(x)
clrs=colorRampPalette(rev(c('darkred', 'red','orange','yellow','cadetblue1', 'cyan', 'dodgerblue4', 'blue','darkorchid1','lightgreen','green', 'forestgreen','darkolivegreen')))(200)
corrplot::corrplot(x, method='color', type='upper', tl.col="black", tl.srt=45, tl.cex = 0.7, diag = FALSE, col=clrs, cl.lim = c(0,1), title = 'Ignore EZ', mar=c(0,0,5,0))
x <- get_pairwise_sharing(m_simple_EZ)
colnames(x) <- colnames(get_lfsr(m_simple_EZ))
rownames(x) <- colnames(x)
corrplot::corrplot(x, method='color', type='upper', tl.col="black", tl.srt=45, tl.cex = 0.7, diag = FALSE, col=clrs, cl.lim = c(0,1), title = 'Simple EZ', mar=c(0,0,5,0))</code></pre>
<p><img src="figure/GTExV6.Rmd/unnamed-chunk-18-1.png" width="1920" style="display: block; margin: auto;" /></p>
<details> <summary><em>Expand here to see past versions of unnamed-chunk-18-1.png:</em></summary>
<table style="border-collapse:separate; border-spacing:5px;">
<thead>
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<th style="text-align:left;">
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<th style="text-align:left;">
Author
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<th style="text-align:left;">
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<td style="text-align:left;">
<a href="https://github.com/zouyuxin/GTEx/blob/5306c8f76093dc136121d237eec1dfd5693cec79/docs/figure/GTExV6.Rmd/unnamed-chunk-18-1.png" target="_blank">5306c8f</a>
</td>
<td style="text-align:left;">
zouyuxin
</td>
<td style="text-align:left;">
2019-01-01
</td>
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<td style="text-align:left;">
<a href="https://github.com/zouyuxin/GTEx/blob/a4437cb53fa9d56504bb2e8176c79f28914b1b17/docs/figure/GTExV6.Rmd/unnamed-chunk-18-1.png" target="_blank">a4437cb</a>
</td>
<td style="text-align:left;">
zouyuxin
</td>
<td style="text-align:left;">
2019-01-01
</td>
</tr>
</tbody>
</table>
<p></details></p>
<pre class="r"><code>par(mfrow=c(1,2))
x <- get_pairwise_sharing(m_current_EZ)
colnames(x) <- colnames(get_lfsr(m_current_EZ))
rownames(x) <- colnames(x)
corrplot::corrplot(x, method='color', type='upper', tl.col="black", tl.srt=45, tl.cex = 0.7, diag = FALSE, col=clrs, cl.lim = c(0,1), title = 'Current EZ', mar=c(0,0,5,0))
x <- get_pairwise_sharing(m_V3_EZ)
colnames(x) <- colnames(get_lfsr(m_V3_EZ))
rownames(x) <- colnames(x)
corrplot::corrplot(x, method='color', type='upper', tl.col="black", tl.srt=45, tl.cex = 0.7, diag = FALSE, col=clrs, cl.lim = c(0,1), title = 'V3 EZ', mar=c(0,0,5,0))</code></pre>
<p><img src="figure/GTExV6.Rmd/unnamed-chunk-19-1.png" width="1920" style="display: block; margin: auto;" /></p>
<details> <summary><em>Expand here to see past versions of unnamed-chunk-19-1.png:</em></summary>
<table style="border-collapse:separate; border-spacing:5px;">
<thead>
<tr>
<th style="text-align:left;">
Version
</th>
<th style="text-align:left;">
Author
</th>
<th style="text-align:left;">
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</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;">
<a href="https://github.com/zouyuxin/GTEx/blob/5306c8f76093dc136121d237eec1dfd5693cec79/docs/figure/GTExV6.Rmd/unnamed-chunk-19-1.png" target="_blank">5306c8f</a>
</td>
<td style="text-align:left;">
zouyuxin
</td>
<td style="text-align:left;">
2019-01-01
</td>
</tr>
<tr>
<td style="text-align:left;">
<a href="https://github.com/zouyuxin/GTEx/blob/a4437cb53fa9d56504bb2e8176c79f28914b1b17/docs/figure/GTExV6.Rmd/unnamed-chunk-19-1.png" target="_blank">a4437cb</a>
</td>
<td style="text-align:left;">
zouyuxin
</td>
<td style="text-align:left;">
2019-01-01
</td>
</tr>
</tbody>
</table>
<p></details></p>
</div>
<div id="session-information" class="section level2">
<h2>Session information</h2>
<pre class="r"><code>sessionInfo()</code></pre>
<pre><code>R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS 10.14.2
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] gridExtra_2.3 ggplot2_3.1.0 kableExtra_0.9.0 knitr_1.20
[5] mashr_0.2.19.0555 ashr_2.2-26 mixsqp_0.1-93 flashr_0.6-3
loaded via a namespace (and not attached):
[1] Rcpp_1.0.0 mvtnorm_1.0-8 lattice_0.20-35
[4] assertthat_0.2.0 rprojroot_1.3-2 digest_0.6.18
[7] foreach_1.4.4 truncnorm_1.0-8 R6_2.3.0
[10] plyr_1.8.4 backports_1.1.2 evaluate_0.12
[13] httr_1.3.1 highr_0.7 pillar_1.3.1
[16] rlang_0.3.0.1 lazyeval_0.2.1 pscl_1.5.2
[19] rstudioapi_0.8 whisker_0.3-2 R.utils_2.7.0
[22] R.oo_1.22.0 Matrix_1.2-14 rmarkdown_1.10
[25] labeling_0.3 readr_1.1.1 stringr_1.3.1
[28] munsell_0.5.0 compiler_3.5.1 pkgconfig_2.0.2
[31] SQUAREM_2017.10-1 htmltools_0.3.6 tidyselect_0.2.5
[34] tibble_1.4.2 workflowr_1.1.1 codetools_0.2-15
[37] viridisLite_0.3.0 crayon_1.3.4 dplyr_0.7.6
[40] withr_2.1.2 MASS_7.3-50 R.methodsS3_1.7.1
[43] grid_3.5.1 gtable_0.2.0 git2r_0.23.0
[46] magrittr_1.5 scales_1.0.0 stringi_1.2.4
[49] reshape2_1.4.3 doParallel_1.0.14 bindrcpp_0.2.2
[52] xml2_1.2.0 rmeta_3.0 iterators_1.0.10
[55] tools_3.5.1 glue_1.3.0 softImpute_1.4
[58] purrr_0.2.5 hms_0.4.2 abind_1.4-5
[61] parallel_3.5.1 yaml_2.2.0 colorspace_1.3-2
[64] rvest_0.3.2 corrplot_0.84 bindr_0.1.1 </code></pre>
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