pre8.split.train.test.batch: Split dataset into TRAIN and TEST files for all files

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

Description

For all files, splits the data files whose names begin with prefix.file, contain a keyword key.file, and end with ending.file, in dir.file into TRAIN and TEST files, based on the percentage train.percent - how many percent of the data should go into TRAIN file.

Usage

pre8.split.train.test.batch(dir.file, dir.out, prefix.file, key.file = "", 
ending.file = ".txt", train.percent = 80, separ = "\t", index.prefix = "index", 
file.has.ext = TRUE, resample = FALSE)

Arguments

dir.file	The name of directory where input files can be found.
dir.out	The name of directory into which the TRAIN and TEST output files should go.
prefix.file	The beginning of the file name for the geno files (up until chrom number).
key.file	Any keyword in the name of the geno files that distinguishes it from other files.
ending.file	The ending of the geno filenames.
train.percent	The pecentage (0 to 100) of what portion of data (rows) should go into the TRAIN file; the rest will be in TEST file. Ex: for 1000 entries, if train.percent=80, then 800 entries will appear in <file.name>.test, and 200 entries will go into <file.name>.train.
separ	The separator used in the file.name to separate entries.
index.prefix	The name of the index file to use for the separation of train from test entries. This file may already exist in dir.out (if it has been created by previous runs of this program).
file.has.ext	Flag whether or not file.name has a filename extension (ex. ".txt", ".ped", ".mlgeno").
resample	Additional file beginning with the name index.prefix will be saved in the dir.out directory for the given train.percent. This file will contain indices that correspond to entries taken into the TRAIN file. If resample=FALSE, then all subsequent runs of this function on other files (for example for different chromosomes on the same dataset) with the same train.percent will use that saved file. This is to make sure that the same individuals go into TRAIN file, across all chromosomes. If resample=TRUE, then new random resampling will take place and new index file will be generated and saved to the dir.out directory; note, in this case the entries generated by this file will no longer correspond to entries generated by previous runs for previous index files; so for consistency, re-run all chromosomes with resample flag set to FALSE.

Details

For all the files in directory dir.file satisfying the naming criterion of prefix.file, key.file, and ending.file, split each of these files into TRAIN and TEST files, based on the percentage train.percent - how many percent of the data should go into TRAIN file.

The input files are expected to have last column represent CASE and CONTROL; this is necessary to make sure that train.percent of CASE and train.percent of CONTROL entries go into TRAIN file, to have even sample of both types of entries. If the data is saved in many files (for example one file per chromosome), this function is designed to first randomly sample the individuals for the TRAIN file for the first file it is run on. Then it uses this sampling for all other chromosomes on subsequent runs (if resample=FALSE), such that individuals in TRAIN file correspond to one another across all chromosome files (same holds for TEST files). The index file is also useful for processing familyl .fam file after the data has been split.

The following files will be output:

 - <file.name>.train.<train.percent>.<ext> - the output TRAIN file containing 
     train.percent percent of the original data; will appear in dir.out directory.
      * <file.name> here is the file name without extension;
      * <ext> is the extension part of <file.name> (i.e. the section that follows
        the last "." symbol)
      * <train.percent> is specifying the percentage that was used to generate 
        the file.
 - <file.name>.test.<train.percent>.<ext> - the entries for TEST file, containing
     the remaining (100 - train.percent) data. Similar to the TRAIN file above.
 - <index.prefix>.<train.percent>.txt - the file containing indicies of the 
     entries corresponding to TRAIN file, this file will be generated if it 
     does not already exist in dir.out, or if resample=TRUE.

Author(s)

Olia Vesselova

See Also

pre6.merge.genos, pre7.add.conf.var, pre8.split.train.test, run1.moss

Examples

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

Example output

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

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