logs_example: Example logs file

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

Example logs file

Description

Example logs file produced by format_sumstats.

Usage

logs_example(read = FALSE)

Arguments

read	Whether to read the logs file into memory.

Value

Path to logs file.

Source

eduAttainOkbayPth <- system.file("extdata", "eduAttainOkbay.txt", package = "MungeSumstats") sumstats_dt <- data.table::fread(eduAttainOkbayPth) #### Introduce values that need to be fixed #### sumstats_dt$Pval[10:15] <- 5 sumstats_dt$Pval[20:22] <- -5 sumstats_dt$Pval[23:25] <- "5e-324" ss_path <- tempfile() data.table::fwrite(sumstats_dt, ss_path) log_folder <- tempdir() reformatted <- MungeSumstats::format_sumstats( path = ss_path, ref_genome = "GRCh37", log_folder = log_folder, log_mungesumstats_msgs = TRUE, log_folder_ind = TRUE, ) file.copy(reformatted$log_files$MungeSumstats_log_msg, "inst/extdata",overwrite = TRUE)

neurogenomics/MungeSumstats documentation built on Aug. 10, 2024, 5:59 a.m.