Usage
pre2.remove.genos.batch(dir.dat, dir.ped = dir.dat, dir.out,
dir.warning = dir.out, perc.snp = 10, perc.patient = 20, empty = "0/0",
num.nonsnp.col = 5, prefix.dat, prefix.case, prefix.control, key.dat = "",
key.case = "CASE", key.control = "CONTROL", ending.dat = ".dat",
ending.case = ".ped", ending.control = ".ped")
Arguments
dir.dat
The directory name where all .dat files can be found.
dir.ped
The directory name where all .ped CASE and CONTROL files can be found. Defaults to same place as dir.dat
dir.out
The directory name to which output files should be saved.
dir.warning
The directory name to which warnings about patients with too many missing SNPs should go. Defaults to the same place as dir.out.
perc.snp
The percentage (0-100 percent) of maximum empty values allowed for each geno (column). All genos that have more empty values than this threshold will be removed.
perc.patient
The percentage (0-100 percent) of empty values allowed for each patient (row). Names of all patients who end up having more empty values than this threshold will be recorded in the warnings file.
empty
The representation of a missing SNP value in the file ("0 0", "0/0", "1/1", "N N", etc).
num.nonsnp.col
The number of leading columns in the .ped files that do not contain SNP values. The first columns of the file represent non-SNP values (like patient ID, gender, etc). For MaCH1 input format, the num.nonsnp.col=5, for PLINK it is 6 (due to extra disease status column).
prefix.dat
The beginning of the file name for the .dat file (up until chrom number).
prefix.case
The beginning of the file name for the CASE pedegree file (up until chrom number).
prefix.control
The beginning of the file name for the CONTROL pedegree file (up until chrom number).
key.dat
Any keyword in the name of the pedegree file that distinguishes it from other files.
key.case
Any keyword in the name of the CASE pedegree file that distinguishes it from other non-pedegree non-CASE files.
key.control
Any keyword in the name of the CONTROL pedegree file that distinguishes it from other non-pedegree non-CONTROL files.
ending.dat
The ending of the .dat filenames.
ending.case
The ending of the CASE pedegree filenames.
ending.control
The ending of the CONTROL pedegree filenames.