pre4.combine.case.control.batch: Combine CASE and CONTROL files for all files

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

Description

For each pair of CASE and CONTROL files, combine them into one file. Last column of each output file will contain the disease status. The disease status is encoded as 1 for CASE and 0 for CONTROL.

Usage

pre4.combine.case.control.batch(dir.file, dir.out = dir.file, prefix.case, 
prefix.control, prefix.out, key.case = "", key.control = "", 
ending.case = ".mlgeno", ending.control = ".mlgeno", separ = " ")

Arguments

dir.file	The name of directory where CASE and CONTROL files can be found.
dir.out	The name of directory to which output file should be written.
prefix.case	The beginning of the file name for the CASE file (up until chrom number).
prefix.control	The beginning of the file name for the CONTROL file (up until chrom number).
prefix.out	The beginning of the file name for the output file (up until chrom number).
key.case	Any keyword in the name of the CASE file that distinguishes it from other files.
key.control	Any keyword in the name of the CONTROL file that distinguishes it from other files.
ending.case	The ending of the CASE filename.
ending.control	The ending of the CONTROL filename.
separ	The separator used in the CASE and CONTROL input files.

Details

The function combines CASE and CONTROL together, attaching disease status as the last column: 1 for CASE and 0 for CONTROL. There will be two output files for each pair of CASE and CONTROL:

 - <dir.out>/<prefix.out><chrom.num><ending.case> - the file containing both 
     CASE and CONTROL values, with the disease status as the last column.
 - <dir.out>/<all.dat> - also will copy over ALL the files ending with ".dat" 
     that exist in \code{\var{dir.file}}.

Author(s)

Olia Vesselova

See Also

pre3.call.mach, pre3.call.mach.batch, pre4.combine.case.control, pre5.genos2numeric, pre5.genos2numeric.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.