R/parse_pval_small.R

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

#' Parse number of SNPs with non-negative p-values <=5e-324
#' 
#' Support function for \link[MungeSumstats]{parse_logs}.
#' 
#' @param l Lines of text from log file.
#' 
#' @return Numeric
#' @keywords internal
parse_pval_small <- function(l){
  line <- grep(
    "p-values are <=5e-324 which LDSC/MAGMA may not be able to handle",l,
    value = TRUE)[1]
  if(is.na(line)) return(NA)
  as.integer(trimws(gsub(",","",strsplit(line," ")[[1]][1])))
}