read.mach

The name of the <code>.mlprob</code> file. This may be gzipped
  

file

The column names. If absent, names are generated as
    <code>SNP1</code>, <code>SNP2</code>, etc.
  

colnames

If known the number of rows of data on the file. If not
    supplied, it is determined by a preliminary pass through the data
  

nrow


This routine reads imputed genotypes generated by the MACH program. With
the <code>--mle</code> and <code>--mldetails</code> options in force this program
generates a
<code>.mlprob</code> output file which contains probabilities of
assignments. These are stored as uncertain genotype calls in a
<code>SnpMatrix</code> object


Classes and statistical methods for large SNP association studies. This extends the earlier snpMatrix package, allowing for uncertainty in genotypes.

David Clayton

snpStats

SnpMatrix and XSnpMatrix classes and methods

read.mach function

The name of the <code>.mlprob</code> file. This may be gzipped

The column names. If absent, names are generated as
    <code>SNP1</code>, <code>SNP2</code>, etc.

If known the number of rows of data on the file. If not
    supplied, it is determined by a preliminary pass through the data

This routine reads imputed genotypes generated by the MACH program. With
the <code>--mle</code> and <code>--mldetails</code> options in force this program
generates a
<code>.mlprob</code> output file which contains probabilities of
assignments. These are stored as uncertain genotype calls in a
<code>SnpMatrix</code> object

read.mach: Read genotypes imputed by the MACH program

Description

Usage

Arguments

Value

Details

See Also

Examples