Question: CRLMM: missing mitochondrial SNPs
gravatar for nadne
2.9 years ago by
nadne10 wrote:

I using the function genotype.Illumina from CRLMM package to calls genotyping raw data files of an Illumina HumanOmni 2.5 SNP array.

g = genotype.Illumina(cdfName='humanomni25quadv1b', path=full_path_dir, call.method='krlmm')
g_c = calls(g)

Now, g_c has 2449907 (one for each SNP). But non of them seems to be a Mitochondrial SNP, even though the analyzed platform has 93 Mitochondrial SNPs. For example, MitoT217C which is also known as rs41531144 does not appear in the recalling object.

How can it be?

crlmm genotype mitochondria • 386 views
ADD COMMENTlink written 2.9 years ago by nadne10
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 309 users visited in the last hour