read.snps.chiamo {snpMatrix} | R Documentation |
This function reads data from the raw output of Chiamo
read.snps.chiamo(filename, sample.list, threshold)
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 |
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.
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 . |
Hin-Tak Leung htl10@users.sourceforge.net
To obtain a copy of the Chiamo software please email Jonathan L. Marchini <marchini@stats.ox.ac.uk>.
wtccc.sample.list
, read.wtccc.signals
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