Last updated: 2022-05-23

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Knit directory: cTWAS_analysis/

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library(gseasusie)
library(tidyverse)
Warning in system("timedatectl", intern = TRUE): running command 'timedatectl'
had status 1
Warning: Your system is mis-configured: '/etc/localtime' is not a symlink
Warning: It is strongly recommended to set envionment variable TZ to 'America/
Chicago' (or equivalent)
genesets <- gseasusie::load_gene_sets(c('gobp'))
library(data.table)
library("AnnotationDbi")
library("org.Hs.eg.db")
data <- fread(file = "data/magma.genes.out")
data$entrez = mapIds(org.Hs.eg.db,
                    keys=data$GENE, #Column containing Ensembl gene ids
                    column="ENTREZID",
                    keytype="ENSEMBL",
                    multiVals="first")

data <- na.omit(data)
data$beta <- 1
data$se <- 1

data <- data[,c("GENE","entrez","P","beta","se","ZSTAT")]
colnames(data) <- c("ENSEMBL","ENTREZID","pvalue","beta","se","threshold.on")
db <- 'gobp' 
thresh = 2  # threshold for binarizing the data
bin.data <- gseasusie::prep_binary_data(genesets[[db]], data, thresh)

X <- bin.data$X
y <- bin.data$y
# fit logistic susie
logistic.fit <- gseasusie::fit_logistic_susie_veb_boost(X, y, L=20)
ELBO: -8075.22
21.905 sec elapsed
# fit linear susie
linear.fit <- susieR::susie(X, y)

# compute odds ratios, and pvalues under hypergeometric (one-sided) and fishers exact (two-sided) tests
ora <- gseasusie::fit_ora(X, y)
14.182 sec elapsed
gseasusie::enrichment_volcano(logistic.fit, ora)

gseasusie::interactive_table(logistic.fit, ora)

sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.3.13-el7-x86_64/lib/libopenblas_haswellp-r0.3.13.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] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] Matrix_1.3-3         org.Hs.eg.db_3.14.0  AnnotationDbi_1.56.1
 [4] IRanges_2.28.0       S4Vectors_0.32.3     Biobase_2.54.0      
 [7] BiocGenerics_0.40.0  data.table_1.14.0    forcats_0.5.1       
[10] stringr_1.4.0        dplyr_1.0.9          purrr_0.3.4         
[13] readr_2.1.2          tidyr_1.2.0          tibble_3.1.7        
[16] ggplot2_3.3.6        tidyverse_1.3.1      gseasusie_0.0.0.9000
[19] workflowr_1.7.0     

loaded via a namespace (and not attached):
  [1] colorspace_2.0-3       ellipsis_0.3.2         rprojroot_2.0.3       
  [4] XVector_0.34.0         fs_1.5.0               rstudioapi_0.13       
  [7] farver_2.1.0           bit64_4.0.5            fansi_1.0.3           
 [10] mvtnorm_1.1-3          lubridate_1.7.10       xml2_1.3.2            
 [13] cachem_1.0.5           knitr_1.33             jsonlite_1.8.0        
 [16] broom_0.7.8            dbplyr_2.1.1           png_0.1-7             
 [19] data.tree_1.0.0        compiler_4.1.0         httr_1.4.3            
 [22] tictoc_1.0.1           backports_1.2.1        assertthat_0.2.1      
 [25] fastmap_1.1.0          cli_3.3.0              later_1.2.0           
 [28] htmltools_0.5.1.1      tools_4.1.0            gtable_0.3.0          
 [31] glue_1.6.2             GenomeInfoDbData_1.2.7 Rcpp_1.0.8.3          
 [34] mr.ash.alpha_0.1-42    cellranger_1.1.0       jquerylib_0.1.4       
 [37] vctrs_0.4.1            Biostrings_2.62.0      crosstalk_1.1.1       
 [40] xfun_0.24              ps_1.6.0               rvest_1.0.0           
 [43] lifecycle_1.0.1        irlba_2.3.5            getPass_0.2-2         
 [46] zlibbioc_1.40.0        scales_1.2.0           hms_1.1.1             
 [49] promises_1.2.0.1       spatstat.utils_2.3-1   parallel_4.1.0        
 [52] emulator_1.2-21        susieR_0.11.92         yaml_2.2.1            
 [55] memoise_2.0.0          sass_0.4.0             reshape_0.8.9         
 [58] stringi_1.7.6          RSQLite_2.2.8          highr_0.9             
 [61] VEB.Boost_0.0.0.9037   GenomeInfoDb_1.30.0    rlang_1.0.2           
 [64] pkgconfig_2.0.3        bitops_1.0-7           matrixStats_0.62.0    
 [67] evaluate_0.14          lattice_0.20-44        htmlwidgets_1.5.3     
 [70] labeling_0.4.2         bit_4.0.4              processx_3.5.2        
 [73] tidyselect_1.1.2       plyr_1.8.7             magrittr_2.0.3        
 [76] R6_2.5.1               generics_0.1.2         DBI_1.1.1             
 [79] pillar_1.7.0           haven_2.4.1            whisker_0.4           
 [82] withr_2.5.0            KEGGREST_1.34.0        RCurl_1.98-1.5        
 [85] mixsqp_0.3-43          reactable_0.2.3        modelr_0.1.8          
 [88] crayon_1.5.1           utf8_1.2.2             tzdb_0.3.0            
 [91] rmarkdown_2.9          grid_4.1.0             readxl_1.4.0          
 [94] reactR_0.4.4           blob_1.2.1             callr_3.7.0           
 [97] git2r_0.28.0           reprex_2.0.0           digest_0.6.29         
[100] httpuv_1.6.1           munsell_0.5.0          bslib_0.2.5.1