Last updated: 2022-04-23

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summary_table <- function(data_path){
  brain_tissue <- list.files(data_path)
  top_genes <- c()
  all_genes <- c()
  for(i in brain_tissue){
    df <- readRDS(paste0(data_path,i,"/SCZ_",i,"_ctwas_gene_res.RDS"))
    all_genes <- c(all_genes,df$genename)
    df <- df[df$susie_pip>=0.8,]
    top_genes <- c(top_genes,df$genename)
  }
  top_genes <- unique(top_genes)
  all_genes <- unique(all_genes)
  set.seed(2022)
  random_genes <- sample(all_genes,1000)
  
  library(readxl)
  Supplementary_Table_15_MAGMA <- read_excel("data/Supplementary Table 15 - MAGMA.xlsx", sheet = "Gene Lists")
  summary_known_genes_annotations <- read_excel("data/summary_known_genes_annotations.xlsx", sheet = "SCZ")
  SCHEMA_genes <- Supplementary_Table_15_MAGMA$`SCHEMA (p<0.001)`
  SCHEMA_genes <- SCHEMA_genes[!is.na(SCHEMA_genes)]
  ASD_genes <- Supplementary_Table_15_MAGMA$`ASD (Satterstrom et al. 2019)`
  ASD_genes <- ASD_genes[!is.na(ASD_genes)]
  DDD_genes <- Supplementary_Table_15_MAGMA$`DDD (Kaplanis et al. 2019)`
  DDD_genes <- DDD_genes[!is.na(DDD_genes)]
  PGC3_genes <- summary_known_genes_annotations$`Gene Symbol`
  PGC3_genes <- PGC3_genes[!is.na(PGC3_genes)]
  
  Supplementary_Table_20_Prioritised_Genes <- read_excel("data/Supplementary Table 20 - Prioritised Genes.xlsx", sheet = "ST20 all criteria")
  SMR_genes <- Supplementary_Table_20_Prioritised_Genes[,c("Symbol.ID","SMRmap","SMRsingleGene","HI.C.SMR")]
  SMR_genes["index"] <- (SMR_genes$SMRmap==1) | (SMR_genes$SMRsingleGene==1) | (SMR_genes$HI.C.SMR==1)
  SMR_genes <- SMR_genes[SMR_genes$index==1,]$Symbol.ID
  
  GO_files <- list.files("data/GO_Terms", pattern="*.txt", full.names=F)
  annotation_table <- as.data.frame(matrix(0,nrow = length(top_genes),ncol = length(GO_files)))
  GO_terms = c()
  for(i in GO_files){GO_terms <- c(GO_terms,unlist(strsplit(i, "\\."))[1])}
  colnames(annotation_table) <- GO_terms
  annotation_table["SCHEMA_genes"] = as.integer(top_genes %in% SCHEMA_genes)
  annotation_table["ASD_genes"] = as.integer(top_genes %in% ASD_genes)
  annotation_table["DDD_genes"] = as.integer(top_genes %in% DDD_genes)
  annotation_table["PGC3_genes"] = as.integer(top_genes %in% PGC3_genes)
  annotation_table["PGC3_genes_without_SMR"] = as.integer(top_genes %in% setdiff(PGC3_genes,SMR_genes))
  annotation_table <- cbind(top_genes,annotation_table)
  annotation_table$top_genes <- as.character(annotation_table$top_genes)

  for(i in 1:length(GO_files)){
    GO_list <- data.table::fread(paste0("data/GO_Terms/",GO_files[i]),header = F)
    for(j in (1:length(top_genes))){
      target_gene <- top_genes[j]
      if(target_gene %in% GO_list$V2){
        annotation_table[j,i] = 1
      }
    }
  }
  annotation_table <- annotation_table[,c("top_genes","SCHEMA_genes","ASD_genes","DDD_genes",
                                        "PGC3_genes","PGC3_genes_without_SMR",GO_terms)]
  
  return(annotation_table)
}

2018 SCZ GWAS

[1] "Number of genes in SCHEMA_genes: 0"
[1] "Number of genes in ASD_genes: 0"
[1] "Number of genes in DDD_genes: 1"
[1] "Number of genes in PGC3_genes: 6"
[1] "Number of genes in PGC3_genes_without_SMR: 1"
[1] "Number of genes in axon: 0"
[1] "Number of genes in ion_channel_complex: 3"
[1] "Number of genes in nervous_system_development: 2"
[1] "Number of genes in neuronal_cell_body: 2"
[1] "Number of genes in regulation_of_cation_channel_activity: 1"
[1] "Number of genes in regulation_of_neuron_differentiation: 2"
[1] "Number of genes in somatodendritic_compartment: 4"
[1] "Number of genes in synapse: 0"
[1] "Number of genes in voltage-gated_calcium_channel_activity: 0"

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:
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 [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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] readxl_1.3.1    reactable_0.2.3 workflowr_1.6.2

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.7        cellranger_1.1.0  pillar_1.6.1      compiler_4.1.0   
 [5] bslib_0.2.5.1     later_1.2.0       jquerylib_0.1.4   git2r_0.28.0     
 [9] highr_0.9         tools_4.1.0       digest_0.6.27     jsonlite_1.7.2   
[13] evaluate_0.14     lifecycle_1.0.0   tibble_3.1.2      pkgconfig_2.0.3  
[17] rlang_0.4.11      crosstalk_1.1.1   yaml_2.2.1        xfun_0.24        
[21] reactR_0.4.4      stringr_1.4.0     knitr_1.33        fs_1.5.0         
[25] vctrs_0.3.8       sass_0.4.0        htmlwidgets_1.5.3 rprojroot_2.0.2  
[29] data.table_1.14.0 glue_1.4.2        R6_2.5.0          fansi_0.5.0      
[33] rmarkdown_2.9     magrittr_2.0.1    whisker_0.4       promises_1.2.0.1 
[37] ellipsis_0.3.2    htmltools_0.5.1.1 httpuv_1.6.1      utf8_1.2.1       
[41] stringi_1.6.2     crayon_1.4.1