Last updated: 2022-04-23
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Knit directory: cTWAS_analysis/
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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)
}[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:
[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] 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