Last updated: 2019-05-30

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Knit directory: gtex-gwas-hki/

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File Version Author Date Message
Rmd ddcbbb2 HKI imac 012 2019-05-28 enloc vs coloc
html ddcbbb2 HKI imac 012 2019-05-28 enloc vs coloc
Rmd d962ff4 HKI imac 012 2019-05-24 enloc vs coloc
html 2452565 HKI imac 012 2019-05-24 enloc vs coloc
Rmd 9fba350 HKI imac 012 2019-05-24 enloc vs coloc

Import libraries and source scripts

print(getwd())
[1] "/Users/haky/Github/gtex-gwas-hki"
# install.packages("bigrquery")
suppressPackageStartupMessages(library(bigrquery))
Warning: package 'bigrquery' was built under R version 3.5.2
# Script with ancillary functions to perform queries to BigQuery
suppressPackageStartupMessages(source("code/BigQuery.R", chdir = TRUE))
Warning: package 'ggplot2' was built under R version 3.5.2
Warning: package 'tibble' was built under R version 3.5.2
Warning: package 'tidyr' was built under R version 3.5.2
Warning: package 'purrr' was built under R version 3.5.2
Warning: package 'stringr' was built under R version 3.5.2
Warning: package 'forcats' was built under R version 3.5.2
##library(tidyverse)
library(readxl)
Warning: package 'readxl' was built under R version 3.5.2
extdata.dir = "~/Desktop/local-analysis/gtex-gwas/data/"

connect to local spark

library(sparklyr)
Warning: package 'sparklyr' was built under R version 3.5.2

Attaching package: 'sparklyr'
The following object is masked from 'package:purrr':

    invoke
sc <- spark_connect(master = "local")
theme_set(theme_bw(base_size=15))

gencode 26 annotation

read pickrell block positions

phenoname = 'UKB_50_Standing_height'
## query enloc/coloc prob
# query <- 'SELECT tissue, phenotype, gene_id, max(rcp) as maxrcp FROM {enloc_tbl$dataset_name}.{enloc_tbl$table_name} where phenotype="{phenoname}" group by tissue, phenotype, gene_id limit 10' %>% glue::glue()


query <- 'SELECT coloc.PP_H4_abf,coloc.tissue, coloc.phenotype, coloc.gene_id,enloc.max_rcp,enloc.nindep FROM `gtex-awg-im.GTEx_V8_COLOC.coloc_with_enloc_priors` as coloc INNER JOIN 
(SELECT tissue, phenotype, gene_id, max(rcp) as max_rcp, count(*) as nindep FROM `gtex-awg-im.GTEx_V8_ENLOC.enloc_all_results` WHERE phenotype="UKB_50_Standing_height" group by tissue, phenotype, gene_id) as enloc
ON coloc.tissue=enloc.tissue and coloc.phenotype=enloc.phenotype and coloc.gene_id = enloc.gene_id WHERE enloc.max_rcp>0.5 OR coloc.PP_H4_abf>0.5 '

df <- query_exec(query, project = multixcan_tbl$project, max_pages = Inf, use_legacy_sql = F) %>% suppressMessages()
Auto-refreshing stale OAuth token.
18.0 gigabytes processed
# df %>% ggplot(aes(max_rcp, PP_H4_abf)) + geom_point()
pp <- df %>% ggplot(aes(max_rcp, PP_H4_abf))+ geom_hline(yintercept=0.5,col='gray',size=2,alpha=.5) + geom_vline(xintercept = 0.5,col='gray',size=2,alpha=.5) + geom_point(size=4,alpha=.3) + theme_bw(base_size = 20) +xlim(0,1)  + ylim(0,1) + xlab("UK Height ENLOC coloc prob") + ylab("UK Height COLOC coloc prob")
print(pp)
Warning: Removed 3 rows containing missing values (geom_point).

## ggsave(paste0(extdata.dir,"figures/height_fine_giant_uk_ALL.png"),width=8,height=8)

tempo_tabla <- df %>% mutate(enloc_uk = max_rcp>0.25, coloc_uk = PP_H4_abf>0.25) %>% select(enloc_uk, coloc_uk) %>% table()

pp  + annotate("text",x=0.125,y=0.625,label=tempo_tabla[1,2],size=10) + annotate("text",x=0.625,y=0.125,label=tempo_tabla[2,1],size=10) + annotate("text",x=0.625,y=0.625,label=tempo_tabla[2,2],size=10)
Warning: Removed 3 rows containing missing values (geom_point).

tempo_tabla <- df %>% filter(nindep==1) %>% mutate(enloc_uk = max_rcp>0.25, coloc_uk = PP_H4_abf>0.25) %>% select(enloc_uk, coloc_uk) %>% table()

pp <- df %>% filter(nindep>1) %>% ggplot(aes(max_rcp, PP_H4_abf))+geom_hline(yintercept=0.5,col='gray',size=2,alpha=.5) + geom_vline(xintercept = 0.5,col='gray',size=2,alpha=.5) + geom_point(size=4,alpha=.3) + theme_bw(base_size = 20) +xlim(0,1)  + ylim(0,1) + xlab("UK Height ENLOC coloc prob") + ylab("UK Height COLOC coloc prob")

pp  + annotate("text",x=0.125,y=0.625,label=tempo_tabla[1,2],size=10) + annotate("text",x=0.625,y=0.125,label=tempo_tabla[2,1],size=10) + annotate("text",x=0.625,y=0.625,label=tempo_tabla[2,2],size=10) + ggtitle("colocs vs enloc uk height single eqtl")

tempo_tabla <- df %>% filter(nindep>1) %>% mutate(enloc_uk = max_rcp>0.25, coloc_uk = PP_H4_abf>0.25) %>% select(enloc_uk, coloc_uk) %>% table()

pp <- df %>% filter(nindep>1) %>% ggplot(aes(max_rcp, PP_H4_abf))+geom_hline(yintercept=0.5,col='gray',size=2,alpha=.5) + geom_vline(xintercept = 0.5,col='gray',size=2,alpha=.5) + geom_point(size=4,alpha=.3) + theme_bw(base_size = 20) +xlim(0,1)  + ylim(0,1) + xlab("UK Height ENLOC coloc prob") + ylab("UK Height COLOC coloc prob")

pp  + annotate("text",x=0.125,y=0.625,label=tempo_tabla[1,2],size=10) + annotate("text",x=0.625,y=0.125,label=tempo_tabla[2,1],size=10) + annotate("text",x=0.625,y=0.625,label=tempo_tabla[2,2],size=10) + ggtitle("colocs vs enloc uk height multiple eqtls")


sessionInfo()
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] patchwork_0.0.1 sparklyr_1.0.0  readxl_1.3.1    forcats_0.4.0  
 [5] stringr_1.4.0   dplyr_0.8.1     purrr_0.3.2     readr_1.3.1    
 [9] tidyr_0.8.3     tibble_2.1.1    ggplot2_3.1.1   tidyverse_1.2.1
[13] bigrquery_1.1.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.1       lubridate_1.7.4  lattice_0.20-38  forge_0.2.0     
 [5] assertthat_0.2.1 rprojroot_1.3-2  digest_0.6.18    R6_2.4.0        
 [9] cellranger_1.1.0 plyr_1.8.4       backports_1.1.4  evaluate_0.13   
[13] httr_1.4.0       pillar_1.4.0     rlang_0.3.4      curl_3.3        
[17] lazyeval_0.2.2   rstudioapi_0.10  whisker_0.3-2    rmarkdown_1.12  
[21] labeling_0.3     config_0.3       r2d3_0.2.3       htmlwidgets_1.3 
[25] bit_1.1-14       munsell_0.5.0    broom_0.5.2      compiler_3.5.1  
[29] modelr_0.1.4     xfun_0.6         pkgconfig_2.0.2  askpass_1.1     
[33] base64enc_0.1-3  htmltools_0.3.6  openssl_1.3      tidyselect_0.2.5
[37] workflowr_1.3.0  crayon_1.3.4     dbplyr_1.4.0     withr_2.1.2     
[41] rappdirs_0.3.1   grid_3.5.1       nlme_3.1-140     jsonlite_1.6    
[45] gtable_0.3.0     DBI_1.0.0        git2r_0.25.2     magrittr_1.5    
[49] scales_1.0.0     cli_1.1.0        stringi_1.4.3    fs_1.3.1        
[53] xml2_1.2.0       ellipsis_0.1.0   generics_0.0.2   tools_3.5.1     
[57] bit64_0.9-7      glue_1.3.1       hms_0.4.2        parallel_3.5.1  
[61] yaml_2.2.0       colorspace_1.4-1 rvest_0.3.3      knitr_1.22      
[65] haven_2.1.0