read.impute {snpStats} | R Documentation

## Read genotypes imputed by the IMPUTE2 program

### Description

The IMPUTE2 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.impute(file, rownames = NULL, nsnp = NULL, snpcol = 2)

### Arguments

`file` | The input file name. This file my be gzipped.
`rownames` | The row names for the output object. Note that these correspond to groups of three columns in the input file. If not supplied, names are generated as `Sample1`, `Sample2` etc.
`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
`snpcol` | Which column of the input will be used as the SNP name. Default is column 2

### Details

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

### See Also

`SnpMatrix-class`

### Examples

    ##---- No example available yet

[Package snpStats version 1.30.0 Index]