pre3.call.mach.batch: Call MaCH imputation with and without Hapmap

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

Description

This is the same program as pre3.call.mach, only it provides an easier way to set function input parameters. This is the only .batch function that does NOT run on all files. Since MaCH computation on each chromosome takes too long, it is faster to process chromosomes in parallel, rather than sequentially. This function imputes all missing values, for details, see pre3.call.mach. NOTE: In this implementation, do NOT run "with Hapmap" - so do NOT provide phases and legend files.

Usage

pre3.call.mach.batch(dir.file, dir.ref = "", dir.out, prefix.dat, prefix.ped, 
prefix.phase = "", prefix.legend = prefix.phase, prefix.out = "result", 
key.dat = "", key.ped = "", key.phase = "", key.legend = "", ending.dat = ".dat", 
ending.ped = ".ped", ending.phase = ".phase", ending.legend = "legend.txt", 
chrom.num, num.iters = 2, num.subjects = 200, step2.subjects = 50, empty = "0/0", 
resample = FALSE, mach.loc = "/software/mach1")

Arguments

dir.file	The name of directory where .ped and .dat files can be found. The format of these files is described in pre3.call.mach
dir.ref	The name of directory where .phase and .legend files have been downloaded to.
dir.out	The name of directory to which output files should go.
prefix.dat	The beginning of the file name for the .dat file (up until chrom number).
prefix.ped	The beginning of the file name for the .ped pedegree file (up until chrom number).
prefix.phase	The beginning of the file name for the phase file (up until chrom number). This file can be obtained from websites like: http://hapmap.ncbi.nlm.nih.gov/downloads/phasing/2007-08_rel22/phased/ or similar/updated versions. No zip. Must be a normal and readable by R file.
prefix.legend	The beginning of the file name for the legend file (up until chrom number). This file can be obtained from same website as phase file. No zip.
prefix.out	The prefix for naming output files that MaCH1 should use. If num.subjects > 0 then the num.subjects will be appended to the prefix name.
key.dat	Any keyword in the name of the .dat file that distinguishes it from other files.
key.ped	Any keyword in the name of the pedegree file that distinguishes it from other files.
key.phase	Any keyword in the name of the phase file that distinguishes it from other files.
key.legend	Any keyword in the name of the legend file that distinguishes it from other files.
ending.dat	The ending of the .dat filename.
ending.ped	The ending of the pedegree filename.
ending.phase	The ending of the phase filename.
ending.legend	The ending of the legend filename.
chrom.num	The chromosome number for which processing should be done.
num.iters	The how many iterations MaCH1 should make in its first step to estimate its model parameters.
num.subjects	How many individuals from the sample should be used for model building by the first step of MaCH1. The random subset of inidividuals will be extracted by this program. Recommended number of subjects is 200-500. Value <= 0 corresponds to using ALL the subjects in the dataset.
step2.subjects	How many individuals should be processed at a time during the second step of MaCH computation. Value <= 0 will use ALL the subjects in the dataset. This variable is important to reduce exponential computation time required by MaCH when number of individuals is too large.
empty	The way a missing/empty entry of SNP is represented in pedegree file.
resample	Whether or not to overwrite the existing file containing the num.subjects entries produced by previous runs of this algorithm with same .dat, .ped, and num.subjects parameters. By default, if the subjects have been sampled before, they are re-used.
mach.loc	The location directory where "mach" executable can be found.

Details

This function imputes all missing values in the data. See pre3.call.mach for details. This is the same program as pre3.call.mach, only it provides an easier way to set function input parameters. Recall that pre3.call.mach function requires users to specify names of .ped, .dat, .phase, and .legend for each chromosome - these files normally would have exactly same names across all chromosomes, and would only differ by the chromosome number. Thus after running pre3.call.mach, for chromosome 1, and in order to run next chromosome (say, chrom "2"), user would need to change this chromosome number in 4 places: from "1" to "2" in .ped, .dat, .phase, and .legend. This function allows user to just change one variable chrom.num, from "1" to "2", and all the other files will be obtained automatically.

This is the only .batch function that does NOT run on all files. Since MaCH computation on each chromosome takes too long, it is faster to process chromosomes in parallel, rather than sequentially. Thus if your dataset is large, then it is recommended to run this function on different computers/nodes for different chromosomes.

Note

In this current version, avoid using Hapmap. So do NOT provide reference and legend files.

Author(s)

Olia Vesselova

References

MaCH website: http://www.sph.umich.edu/csg/abecasis/MACH/download/

See Also

pre2.remove.genos, pre2.remove.genos.batch, pre3.call.mach, pre4.combine.case.control, pre4.combine.case.control.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.