get_boot_pvals_fec.R

# Get Final results from bootstrapping and ML
# SAS fecundity

# updated - 3/28/24

#Remove scientific notation
#options(scipen = 999)  
options(warn=1)

#Argument, libraries, and settings
suppressMessages(library("optparse")) #load opt parser library
suppressMessages(library("dplyr"))
suppressMessages(library("data.table"))

option_list = list(
  make_option(c("-m", "--mlfile"), type="character", default=NULL, 
              help="ML results file (.maxl)", metavar="character"),
  make_option(c("-b", "--bootfile"), type="character", default=NULL, 
              help="bootstrap file (.boot)", metavar="character"),
  make_option(c("-o", "--output"), type="character", default=NULL, 
              help="output file name", metavar="character")
); 

opt_parser = OptionParser(option_list=option_list);
opt = parse_args(opt_parser);

if (is.null(opt$mlfile)){
  print_help(opt_parser)
  stop("At least one argument must be supplied (input maxl file).n", 
    call.=FALSE)
}
if (is.null(opt$output)){
  print_help(opt_parser)
  stop("At least one argument must be supplied (output file name).n", 
    call.=FALSE)
}

### Import functions
source('/scratch/ukb/scripts/ML_functions.R')

#ML file
ml_output <- fread(opt$mlfile, sep="\t", header = TRUE, check.names=FALSE)

## UPLOAD BOOTS FILE

boot <- fread(opt$bootfile, sep="\t", header = TRUE, check.names=FALSE)

#get p-values from bootstrapping
snpids <- as.vector(unique(ml_output$Site1_SNP))
p_boot_dist <- data.frame()
out1 <- lapply(snpids,get_boot_p.f,bootdist=boot,est=ml_output)
p_boot_dist <- do.call(rbind, out1)


#combine with ML results
f_output <- merge(ml_output, p_boot_dist, by="Site1_SNP")
f_output <- f_output %>% select(Chrom,Window,Site1_Position,Site1_SNP,
  Site1_MAF,Site1_Allele0,Site1_Allele1,
  Site0_Position,Site0_SNP,Site0_MAF,Site0_Allele0,Site0_Allele1,
  s_int_fecundity = s_f_int, SE_f, Z_f, Pval_int_boot_fecundity = P_f,
  s_site1_fecundity =  s_f_site1, s_site0_fecundity =  s_f_site0)
f_output[order(f_output$Window),] -> f_output

#Output
write.table(f_output, paste0(opt$output, ".f.result"), row.names = FALSE, sep="\t")