Last updated: 2017-03-30

Code version: 089055d

The result for FLASH on GTEx data is on midway cluster

Zsocre data

To get the zscore data:

scp username@midway2.rcc.uchicago.edu:/project/mstephens/flash/eQTLzscore/gtexEQTL_zscore.rds ./

and then open Rstudio

load("gtexEQTL_zscore.rds")

the matrix zscore is the data matrix.

FLASH result

constant variance

scp username@midway2.rcc.uchicago.edu:/project/mstephens/flash/eQTLzscore/bflashconst.rds ./

column-wise variance

scp username@midway2.rcc.uchicago.edu:/project/mstephens/flash/eQTLzscore/bflashvarcol.rds ./

constant variance + known variance structure

scp username@midway2.rcc.uchicago.edu:/project/mstephens/flash/eQTLzscore/bflashnoisyConst.rds ./

column-wise variance + known variance structure

scp username@midway2.rcc.uchicago.edu:/project/mstephens/flash/eQTLzscore/bflashnoisycol.rds ./

load the result

we load the column-wise variance reslut which we use in our paper as example

load("bflashvarcol.rds")

and the list b_flash is the reslut of backfitting FLASH with estimation of \(l\) \(f\) and \(\hat{\Sigma}_e\)

plot the barplot

this is from Gao:

data set: /project/mstephens/data/internal_supp/gtex-v6-sumstat-hdf5

[5:25]
on midway. you can focus on MatrixEQTLSumStats.Portable.h5

[5:26]
for the 16000 times 44 data-set, stored in a table called max (edited)

[5:26]
To process the data, https://github.com/stephenslab/gtex-eqtls/blob/master/doc/notes/SumstatsDB.md

[5:27]
and the relevent scripts in this MD file: https://github.com/stephenslab/lab-resource/blob/master/utilities/src/SumstatQuery.R

[5:30]
you should use this line GetSS("max", "/project/mstephens/gtex/analysis/april2015/query/MatrixEQTLSumStats.h5")

—– October 20th, 2016 —– gaow [6:06 PM] https://github.com/stephenslab/lab-resource/wiki/Tissue-Color-Palette

[6:06]
see “load to R”

Session information

sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.12.3 (unknown)

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] workflowr_0.4.0 rmarkdown_1.3   cowplot_0.7.0   ggplot2_2.2.1  

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.9      rprojroot_1.2    digest_0.6.12    assertthat_0.1  
 [5] grid_3.3.0       plyr_1.8.4       backports_1.0.5  gtable_0.2.0    
 [9] git2r_0.18.0     magrittr_1.5     evaluate_0.10    scales_0.4.1    
[13] stringi_1.1.2    lazyeval_0.2.0   rstudioapi_0.6   labeling_0.3    
[17] tools_3.3.0      stringr_1.2.0    munsell_0.4.3    yaml_2.1.14     
[21] colorspace_1.3-2 htmltools_0.3.5  knitr_1.15.1     tibble_1.2

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