read.snps.chiamo: Read genotype data from the output of Chiamo

In chopsticks: The 'snp.matrix' and 'X.snp.matrix' Classes

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 [e-mail]

References

To obtain a copy of the Chiamo software please email Jonathan L. Marchini <[e-mail]>.

See Also

wtccc.sample.list, read.wtccc.signals

Examples

#

Example output

Loading required package: survival
Warning message:
In methods:::bind_activation(TRUE) :
  methods:::bind_activation(TRUE) is deprecated;
 you should rather provide methods for cbind2() / rbind2()

chopsticks documentation built on Nov. 8, 2020, 7:51 p.m.