pre0.dir.create: Generate working subdirectory structure

Description

Function to help create the recommended subdirectory structure for the pre-processing. In dir.out a directory with name out.name will be created. Inside of this out.name directory will be a set of subdirectories, whose names will begin with prefix.dir, followed by a number, followed by short description of what the folder is designed to contain.

Usage

pre0.dir.create(dir.out = ".", out.name = "newdata", prefix.dir = "d")

Arguments

dir.out

The name of directory to which new folder out.name should be saved.

out.name

The name of the new working directory.

prefix.dir

The start of the name of all subdirectories that will be located inside out.name folder.

Value

out$d0: The name of subdirectory into which original data should be placed.
out$d1: The name of subdirectory into which data converted into Plink format should go. This can be done by function similar to ex2plink.
out$d2: The name of subdirectory into which data converted into MaCH input format should go. This can be done by pre1.plink2mach.batch.
out$d3: The name of subdirectory into which data with removed empty SNPs should go. This can be done by pre2.remove.genos.batch.
out$d4: The name of subdirectory into which reference files needed for MaCH1 can be downloaded (if needed).
out$d5: The name of subdirectory into which output of MaCH1 should go. This can be done by pre3.call.mach.batch.
out$d6: The name of subdirectory into which combined CASE and CONTROL files should go. This can be done by pre4.combine.case.control.batch.
out$d7: The name of subdirectory into which data converted to numeric 3 levels should go. This can be done by pre5.genos2numeric.batch.
out$d8: The name of subdirectory into which numeric data merged across all chromosomes should go. This can be done by pre6.merge.genos.
out$d9: The name of subdirectory into which data appended with confounding variable information would go (if there is confounding variable info). This can be done by pre7.add.conf.var.
out$d10: The name of subdirectory into which merged data split into train and test sets should go (if the split is desired). The train-test split can be done by pre8.split.train.test.batch.
out$d11: The name of subdirectory into which desired subsets of the data should go. The extraction of data subset can be done by tune1.subsets.

Details

The subdirectory structure is designed to easily work with preprocessing functions of GenMOSS. Since GenMOSS preprocessing steps need to be performed in a fixed order, and there are several files per chromosome at each step, very good organization of these files is necessary to know what files have come from where and which .dat, .ped, and .fam files correspond. This function creates the directory and subdirectory structure, and it also returns the names of all the subdirectories, which can be easily used as out$d0 to out$d11. See the demo "gendemo" that shows how to effortlessly use this return variable when calling all the pre-processing steps.

Examples

Run this code

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

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