CorShrink

Session information

Last updated: 2019-01-24

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✔ Repository version: e42436d
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```
Ignored files:
    Ignored:    .DS_Store
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    data/.DS_Store
    Ignored:    output/.DS_Store

Untracked files:
    Untracked:  code/Demo_SumstatQuery.R
    Untracked:  data/cor_tissues_non_ash_voom_pearson.rda
    Untracked:  data/gene_names_GTEX_V6.txt
    Untracked:  data/genewide_ash_out_tissue_mat_halfuniform_non_mode.rda
    Untracked:  data/order_index.rda
    Untracked:  data/samples_id.txt
    Untracked:  data/tissuewide_pearson_halfuniform_tissuewide_non_mode.rda
    Untracked:  output/GTExV6/
    Untracked:  output/corshrink_noise_gene_1.rds

Unstaged changes:
    Modified:   analysis/GTExV6.Rmd
```
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File	Version	Author	Date	Message
Rmd	e42436d	zouyuxin	2019-01-24	wflow_publish(“analysis/CorShrinkEQTL.Rmd”)
html	0db93a9	zouyuxin	2019-01-23	Build site.
Rmd	45a32c7	zouyuxin	2019-01-23	wflow_publish(“analysis/CorShrinkEQTL.Rmd”)
html	65128e5	zouyuxin	2019-01-23	Build site.
Rmd	a210b81	zouyuxin	2019-01-23	wflow_publish(“analysis/CorShrinkEQTL.Rmd”)
html	6604682	zouyuxin	2019-01-23	Build site.
Rmd	a7a08cc	zouyuxin	2019-01-23	wflow_publish(“analysis/CorShrinkEQTL.Rmd”)
html	b78df8e	zouyuxin	2019-01-23	Build site.
Rmd	d881589	zouyuxin	2019-01-23	wflow_publish(“analysis/CorShrinkEQTL.Rmd”)

library(mashr)

Loading required package: ashr

library(corrplot)

corrplot 0.84 loaded

library(ggplot2)
library(gridExtra)

gtex <- readRDS(gzcon(url("https://github.com/stephenslab/gtexresults/blob/master/data/MatrixEQTLSumStats.Portable.Z.rds?raw=TRUE")))

V.kushal.tissuewide = readRDS('output/GTExV6/V_strong_tissuewide.rds')

V.null.tissuewide = readRDS('output/GTExV6/V_corshrink_array.rds')

m_current_EZ = readRDS('output/GTExV6/m_current_EZ_post.rds')
m_current_EZ_weights = readRDS('output/GTExV6/m_current_EZ_post_weights.rds')$posterior_weights
m_V3_EZ_tissuewide = readRDS('output/GTExV6/m_V3_tissuewide_EZ.rds')
m_V3_EZ_tissuewide$result = readRDS('output/GTExV6/m_V3_tissuewide_EZ_post_weights.rds')$posterior_matrices

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)

sign = get_significant_results(m_current_EZ)
gene_names = dimnames(V.null.tissuewide)[[3]]
numg = 8265

The left plot is the original effect estimate for a single tissue. The middle plot is the mash estimates with a globel estimate of V. The right plot is the mash estimates with gene-specific noise correlation (CorShrink result from Kushal).

stronggene = data.frame(gtex$strong.b[numg,])
colnames(stronggene) = 'EffectSize'
stronggene$Group = row.names(stronggene)
stronggene$se = gtex$strong.s[numg,]
p1 = ggplot(stronggene, aes(y = EffectSize, x = Group)) + 
  geom_point(show.legend = FALSE, color=gtex.colors) + coord_flip() + ggtitle('PLIN1 ENSG00000166819') + ylim(c(-0.8,1)) + 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[numg,])
colnames(stronggeneCurrent) = 'EffectSize'
stronggeneCurrent$Group = row.names(stronggeneCurrent)
stronggeneCurrent$se = m_current_EZ$result$PosteriorSD[numg,]
p2 = ggplot(stronggeneCurrent, aes(y = EffectSize, x = Group)) + 
  geom_point(show.legend = FALSE, color=gtex.colors) + ylim(c(-0.8,1)) + coord_flip() + ggtitle('ENSG00000166819 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_tissuewide$result$PosteriorMean[numg,])
colnames(stronggeneV3) = 'EffectSize'
stronggeneV3$Group = row.names(stronggeneV3)
stronggeneV3$se = m_V3_EZ_tissuewide$result$PosteriorSD[numg,]
p3 = ggplot(stronggeneV3, aes(y = EffectSize, x = Group)) + 
  geom_point(show.legend = FALSE, color=gtex.colors) + ylim(c(-0.8,1)) + coord_flip() + ggtitle('ENSG00000166819 V3 tissuewide') + 
  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)

Expand here to see past versions of unnamed-chunk-3-1.png:

Version	Author	Date
6604682	zouyuxin	2019-01-23
b78df8e	zouyuxin	2019-01-23

par(mfrow=c(1,2))
col2 <- c("blue", "white", "red")

tmp = V.null.tissuewide[,,numg]
colnames(tmp) = row.names(stronggene)
row.names(tmp) = colnames(tmp)
g1 <- corrplot(tmp, 
               col = colorRampPalette(col2)(200),
               tl.pos = "td", tl.cex = 0.7, tl.col = gtex.colors,
               rect.col = "white",na.label.col = "white",
               method = "color", type = "upper") 

tmp = V.kushal.tissuewide[,,numg]
colnames(tmp) = row.names(stronggene)
row.names(tmp) = colnames(tmp)
g2 <- corrplot(tmp, 
               col = colorRampPalette(col2)(200),
               tl.pos = "td", tl.cex = 0.7, tl.col = gtex.colors,
               rect.col = "white",na.label.col = "white",
               method = "color", type = "upper")

Expand here to see past versions of unnamed-chunk-4-1.png:

Version	Author	Date
0db93a9	zouyuxin	2019-01-23
65128e5	zouyuxin	2019-01-23
b78df8e	zouyuxin	2019-01-23

numg = 10500
stronggene = data.frame(gtex$strong.b[numg,])
colnames(stronggene) = 'EffectSize'
stronggene$Group = row.names(stronggene)
stronggene$se = gtex$strong.s[numg,]
p1 = ggplot(stronggene, aes(y = EffectSize, x = Group)) + 
  geom_point(show.legend = FALSE, color=gtex.colors) + coord_flip() + ggtitle('ENSG00000186523') + ylim(c(-0.6,1.5)) + 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[numg,])
colnames(stronggeneCurrent) = 'EffectSize'
stronggeneCurrent$Group = row.names(stronggeneCurrent)
stronggeneCurrent$se = m_current_EZ$result$PosteriorSD[numg,]
p2 = ggplot(stronggeneCurrent, aes(y = EffectSize, x = Group)) + 
  geom_point(show.legend = FALSE, color=gtex.colors) + ylim(c(-0.6,1.5)) + coord_flip() + ggtitle('ENSG00000186523 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_tissuewide$result$PosteriorMean[numg,])
colnames(stronggeneV3) = 'EffectSize'
stronggeneV3$Group = row.names(stronggeneV3)
stronggeneV3$se = m_V3_EZ_tissuewide$result$PosteriorSD[numg,]
p3 = ggplot(stronggeneV3, aes(y = EffectSize, x = Group)) + 
  geom_point(show.legend = FALSE, color=gtex.colors) + ylim(c(-0.6,1.5)) + coord_flip() + ggtitle('ENSG00000186523 V3 tissuewide') + 
  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)

par(mfrow=c(1,2))
col2 <- c("blue", "white", "red")

tmp = V.null.tissuewide[,,numg]
colnames(tmp) = row.names(stronggene)
row.names(tmp) = colnames(tmp)
g1 <- corrplot(tmp,
               col = colorRampPalette(col2)(200),
               tl.pos = "td", tl.cex = 0.7, tl.col = gtex.colors,
               rect.col = "white",na.label.col = "white",
               method = "color", type = "upper") 

tmp = V.kushal.tissuewide[,,numg]
colnames(tmp) = row.names(stronggene)
row.names(tmp) = colnames(tmp)
g2 <- corrplot(tmp, 
               col = colorRampPalette(col2)(200),
               tl.pos = "td", tl.cex = 0.7, tl.col = gtex.colors,
               rect.col = "white",na.label.col = "white",
               method = "color", type = "upper")

Session information

sessionInfo()

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     corrplot_0.84     mashr_0.2.19.0555
[5] ashr_2.2-26      

loaded via a namespace (and not attached):
 [1] tidyselect_0.2.5  purrr_0.2.5       lattice_0.20-38  
 [4] colorspace_1.4-0  htmltools_0.3.6   yaml_2.2.0       
 [7] rlang_0.3.1       R.oo_1.22.0       mixsqp_0.1-93    
[10] pillar_1.3.1      glue_1.3.0        withr_2.1.2      
[13] R.utils_2.7.0     bindrcpp_0.2.2    foreach_1.4.4    
[16] plyr_1.8.4        bindr_0.1.1       stringr_1.3.1    
[19] munsell_0.5.0     gtable_0.2.0      workflowr_1.1.1  
[22] R.methodsS3_1.7.1 mvtnorm_1.0-8     codetools_0.2-16 
[25] evaluate_0.12     labeling_0.3      knitr_1.20       
[28] pscl_1.5.2        doParallel_1.0.14 parallel_3.5.1   
[31] Rcpp_1.0.0        backports_1.1.3   scales_1.0.0     
[34] rmeta_3.0         truncnorm_1.0-8   abind_1.4-5      
[37] digest_0.6.18     stringi_1.2.4     dplyr_0.7.8      
[40] grid_3.5.1        rprojroot_1.3-2   tools_3.5.1      
[43] magrittr_1.5      lazyeval_0.2.1    tibble_2.0.1     
[46] crayon_1.3.4      whisker_0.3-2     pkgconfig_2.0.2  
[49] MASS_7.3-51.1     Matrix_1.2-15     SQUAREM_2017.10-1
[52] assertthat_0.2.0  rmarkdown_1.11    iterators_1.0.10 
[55] R6_2.3.0          git2r_0.24.0      compiler_3.5.1

This reproducible R Markdown analysis was created with workflowr 1.1.1

CorShrink

Yuxin Zou

1/23/2019

Session information