genMOSSplus (version 1.0)

pre7.add.conf.var.unix: Append confounding variables using Linux

Description

Uses Linux functions to append confounding variables listed in file.conf to the end of the file.name, right before the disease status (last) column. The output will contain only the patients for which confounding variables exist (other patients will be omitted), so new family file will be written. This function is similar to pre7.add.conf.var, only it avoids having to load up into memory the file.name (since this file can be very large).

Usage

pre7.add.conf.var.unix(file.name, dir.file, file.fam, dir.fam = dir.file, 
file.conf, dir.conf = dir.file, file.out, fam.out = file.fam, dir.out)

Arguments

file.name

The name of the data file. The format of this file should have last column as the disease status, tab separated, no header.

dir.file

The name of directory where file.name can be found.

file.fam

The name of the family file. Format: one column - one patient ID per line.

dir.fam

The name of directory where file.fam can be found.

file.conf

The name of the file that contains confounding variable information. The file should be in the following format:

    patientID1 1       2 ...
    patientID2 3       1 ...
    patientID3 2       2 ...
    ...
    - Column 1: patient ID, exactly the same names should appear in 
	file.fam;
               * order does not matter;
               * some patients may be missing;
               * no new patients should appear in file.conf (if they 
		don't exist in file.fam)
    - Column 2: the confounding variable must have no more than 3 
	different values.
    - Other columns are optional, may be included if there are 
	more confounding variables (3 categories each)
    - No header
    - Tab separated
    - No missings or NAs

dir.conf

The name of directory where file.conf can be found.

file.out

The name of the output file, which will contain all information of file.name, plus confounding variables, only for the patients mentioned in file.conf.

fam.out

The name of the family output file.

dir.out

The name of directory to which file.out and fam.out should be saved.

See Also

pre7.add.conf.var, pre6.merge.genos, pre8.split.train.test, pre8.split.train.test.batch

Examples

print("See the demo 'gendemo'.")