read.snpdata.minimac

a filename root to which suffixes (my default <code>.info.gz</code> and <code>.dose.gz</code>)
    will be appended.

fileroot

a tolerence for checking allele frequencies between the
    two files read.

tol.af

if not <code>NULL</code>, 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.

phenotypes

a suffix to add to the filename root to make the name
    of the info file

isuffix

a suffix to add to the filename root to make the name
    of the dosage file

dsuffix


  Reads snp coding information and genotype data from paired
  <code>.info.gz</code> and <code>.dose.gz</code> files, as generated by the MACH and
  minimac genotype imputation programs, and returns the data in a
  standard format (see <a rd-options="" href="/link/snpdata?package=gtx&version=0.0.8" data-mini-rdoc="gtx::snpdata">snpdata</a>) that can be used by other
  functions in this package.


Assorted tools for genetic association analyses.  The
current focus is on implementing (either exactly or
approximately) regression analyses using summary statistics
instead of using subject-specific data.  So far, functions
exist to support multi-SNP risk score analyses, multi-SNP
conditional regression analyses, and multi-phenotype analyses,
using summary statistics.  There are helper functions for
reading and manipulating subject-specific genotype data, which
provide a platform for calculating the summary statistics, or
for using R to conduct other analyses not supported by specific
GWAS analysis tools.

read.snpdata.minimac: Read genotype dosages in the format output by minimac

Description

Usage

Arguments

Value

Details

References