chopsticks (version 1.36.0)

read.snps.chiamo: 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

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.

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.

References

To obtain a copy of the Chiamo software please email Jonathan L. Marchini .

See Also

wtccc.sample.list, read.wtccc.signals

Examples

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