snpStats: read.beagle – R documentation

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read.beagle

Read genotypes imputed by the BEAGLE program

Description

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

Usage

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

Arguments

`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)

Details

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

Value

an object of class SnpMatrix

Author(s)

David Clayton dc208@cam.ac.uk

Examples

##---- No example available yet

snpStats

SnpMatrix and XSnpMatrix classes and methods

v1.40.0

GPL-3

Authors

David Clayton <dc208@cam.ac.uk>

Initial release

2019-10-08