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

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

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="" dataset.="" this="" variable="" is="" important="" to="" reduce="" exponential="" computation="" time="" required by="" mach="" when="" number="" of="" individuals="" too="" large.<="" p="">

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.

References

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

Examples

Run this code

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

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