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

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/read.chiamo.R

Description

This function reads data from the raw output of Chiamo

Usage

1
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

1
#

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 April 29, 2020, 5:24 a.m.