read.beagle: Read genotypes imputed by the BEAGLE program
In NikNakk/snpStats: SnpMatrix and XSnpMatrix classes and methods

Description Usage Arguments Details Value Author(s) See Also Examples

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

1	read.beagle(file, rownames=NULL, nsnp = NULL, header=TRUE)

`file`	The input file name. This file my be gzipped.
`rownames`	The row names (sample identifiers) for the matrix
`nsnp`	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
`header`	Set this `TRUE` if the file contains a header line (it won't for older versions of BEAGLE)

In later versions of BEAGLE, row names are listed on a header line. However, if the rownames argument is supplied, this will take precedence over the header line. If there is no header line and no row names are supplied, names are generated as Sample1, Sample2 etc.

No provision is made for data for the X chromosome. Such data must be first read as a SnpMatrix and subsequently coerced to an XSnpMatrix object

an object of class SnpMatrix

David Clayton dc208@cam.ac.uk

SnpMatrix-class