read.mach {snpStats} | R Documentation

## Read genotypes imputed by the MACH program

### Description

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

### Usage

    read.mach(file, colnames = NULL, nrow = NULL)

### Arguments

`file` | The name of the `.mlprob` file. This may be gzipped
`colnames` | The column names. If absent, names are generated as `SNP1`, `SNP2`, etc.
`nrow` | If known the number of rows of data on the file. If not supplied, it is determined by a preliminary pass through the data

### Details

No routine is explicitly available for data on chromosome X. Such data should first be read as a `SnpMatrix` and then 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]