read.snps.chiamo {chopsticks} | R Documentation

## Read genotype data from the output of Chiamo

### Description

This function reads data from the raw output of Chiamo

### Usage

    read.snps.chiamo(filename, sample.list, threshold)

### Arguments

`filename` | List of file names of output from Chiamo ; the outcome is the concatenation from runs of Chiamo, e.g. on blocks of SNPs, which is often done for practical reasons
`sample.list` | A character vector giving the sample list
`threshold` | Cut-off for the posterior probability for a no-call

### Details

The raw output of Chiamo consists of the first 5 columns of `read.wtccc.signals`, followed by triplets of posterior probabilities of calling A-A, A-B, or B-B.

The sample list can typically be obtained using `wtccc.sample.list`, from one of the (smaller) signal files, which are the inputs to Chiamo.

### Value

The result is a list of two items:

`snp.data` | The genotype data as a `snp.matrix-class` object.
`snp.support` | The information from the first 5 columns of `read.wtccc.signals`.

### Author(s)

Hin-Tak Leung htl10@users.sourceforge.net

### References

To obtain a copy of the Chiamo software please email Jonathan L. Marchini <marchini@stats.ox.ac.uk>.

### See Also

`wtccc.sample.list`, `read.wtccc.signals`

### Examples

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[Package chopsticks version 1.52.0 Index]