pre7.add.conf.var: Append confounding variables

In genMOSSplus: Application of MOSS algorithm to genome-wide association study (GWAS)

Description

Appends 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.

Usage

pre7.add.conf.var(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.

Author(s)

Olia Vesselova

See Also

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

Examples

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

Example output

[1] "See the demo 'gendemo'."

genMOSSplus documentation built on May 1, 2019, 10:31 p.m.