read.snpdata.mach

a filename root to which <code>.mlinfo</code> and <code>.mldose</code>
    extensions 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

Reads snp coding information and genotype data from paired
  <code>.mlinfo</code> and <code>.mldose</code> files, as generated by the MACH and
  minimac genotype imputation programs, and returns the data in a
  standard format (see <a href="/link/snpdata?package=gtx&version=0.0.3" rd-options="" data-mini-rdoc="gtx::snpdata">snpdata</a>) that can be used by other
  functions in this package.

Assorted tools for genetic association analyses.  The 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, and multi-SNP conditional regression 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.mach: Read genotype dosages in the format output by MACH

Description

Usage

Arguments

Value

Details

References