read.snpdata.mach: Read genotype dosages in the format output by MACH
In gtx: Genetics ToolboX

Description Usage Arguments Details Value Author(s) References

Reads snp coding information and genotype data from paired .mlinfo and .mldose files, as generated by the MACH and minimac genotype imputation programs, and returns the data in a standard format (see snpdata) that can be used by other functions in this package.

1 2	read.snpdata.mach(fileroot, tol.af = 0.01, phenotypes = NULL, isuffix = ".mlinfo", dsuffix = ".mldose")

`fileroot`	a filename root to which suffixes (my default `.mlinfo` and `.mldose`) will be appended.
`tol.af`	a tolerence for checking allele frequencies between the two files read.
`phenotypes`	if not `NULL`, a data frame of phenotypes to be merged with the genotypes; must contain a column called MACHID which is used to match against the first column of the mldose file.
`isuffix`	a suffix to add to the filename root to make the name of the info file
`dsuffix`	a suffix to add to the filename root to make the name of the dosage file

This function will (just) work as is with HapMap imputed single chromosomes and 4000 individuals. Need to comment on how to extract large numbers of SNPs before feeding to R.

If isuffix or dsuffix end in .gz extensions, the files will be decompressed on the fly.

Returns a list with snpinfo and data slots, see snpdata.

Toby Johnson Toby.x.Johnson@gsk.com

Information about the MACH and minimac programs for genotype imputation, including their output formats, can be found at http://www.sph.umich.edu/csg/abecasis/MACH.

gtx documentation built on May 2, 2019, 5:08 a.m.