R/Zscore_sumstats.R

In RajLabMSSM/echofinemap: echoverse module: Fine-mapping functions

Zscore_sumstats <- function(fullSS="./Data/GWAS/Nalls23andMe_2019/nallsEtAl2019_allSamples_allVariants.mod.txt",
                           target_col="statistic",
                           effect_col="beta",
                           stderr_col="se",
                           use_saved=TRUE,
                           output_path="./Data/GWAS/Nalls23andMe_2019/z.info.RDS"){
    if(use_saved & file.exists(output_path)){
        printer("Reading in:",output_path,"...")
        z.info <- readRDS(output_path) 
    } else { 
        printer("Extracting mean and standard deviation from",fullSS,"...")
        if(target_col=="calculate"){
            target_col <- "t_stat"
            sample_x <- data.table::fread(fullSS, nThread = 4, 
                                          select=c(effect_col, stderr_col), 
                                          col.names = c("Effect","StdErr"))
            sample_x <- subset(calculate.tstat(sample_x), select = target_col) 
        }else {
            sample_x <- data.table::fread(fullSS, nThread = 4, select=c(target_col))
        } 
        sample.mean <- mean(sample_x[[1]], na.rm = T)
        sample.stdv <- sd(sample_x[[1]])
        z.info <- list(file.name=fullSS,
                       colname=target_col,
                       sample.mean=sample.mean, 
                       sample.stdv=sample.stdv,
                       sample.min=min(sample_x[[1]]),
                       sample.max=max(sample_x[[1]])) 
        saveRDS(z.info, file = output_path )
    } 
    return(z.info)
}