read.beagle


    The input file name. This file my be gzipped.
  

file


    The row names (sample identifiers) for the matrix
    

rownames


    The number of SNPs to be read in. This corresponds with the number
    of lines in the input file. If not supplied, the function does a
    preliminary pass to determine the number of lines
  

nsnp


    Set this <code>TRUE</code> if the file contains a header line (it won't
    for older versions of BEAGLE)
  

header


The BEAGLE program generates, for each SNP and each subject, 
posterior probabilities for the three genotypes. This function reads
such data as a <code>SnpMatrix</code> object, storing the posterior
probabilities to as much accuracy allowed by a one-byte coding


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.beagle function

The input file name. This file my be gzipped.

The row names (sample identifiers) for the matrix

The number of SNPs to be read in. This corresponds with the number
    of lines in the input file. If not supplied, the function does a
    preliminary pass to determine the number of lines

Set this <code>TRUE</code> if the file contains a header line (it won't
    for older versions of BEAGLE)

The BEAGLE program generates, for each SNP and each subject, 
posterior probabilities for the three genotypes. This function reads
such data as a <code>SnpMatrix</code> object, storing the posterior
probabilities to as much accuracy allowed by a one-byte coding

read.beagle: Read genotypes imputed by the BEAGLE program

Description

Usage

Arguments

Value

Details

See Also

Examples