X-chromosome inactivation model in SNPTEST

Question

[krishnapashu912]

Hi,

I am trying to include X-chromosome in Genome-Wide Association Analysis with X-inactivation model with SNPTEST. SNPTEST webpage says - "When using -method newml for case/control traits, SNPTEST ignores samples with missing sex and assumes a model of full X inactivation by default."

However, I am working with continuous phenotype and not able to figure out the way to add a model of full X inactivation. Could anyone please help me with this!

best wishes, krishna

[Kevin Blighe]

The webpage is just stating that it will assume full X inactivation if you do not supply the gender/sex. Do you have the sex/gender of your study participants?

Later on the webpage (https://mathgen.stats.ox.ac.uk/genetics_software/snptest/snptest.html#X_chromosome), they state:

By default, sex information is taken from a column named "sex" in the sample file, and males are coded in the input file in the same way as homozygote females. The -sex_column and -haploid_genotype_coding options can be used to adjust this behaviour.

[krishnapashu912]

Thanks for the reply! Yes, I do have gender of study participants. Does that mean I remove the gender column from phenotype data for full X-inactivation assumption?

[Kevin Blighe]

The way that they phrase it on the website is not 100% clear and I would still encourage you to seek clarification from the authors of the program.

Reading it again, I can interpret their statement in 2 ways for when using -method newml:

• samples that have missing sex/gender will be removed from the study. All other samples (that have sex/gender information) will be assumed to have full X inactivation
• samples that have missing sex/gender will be assumed to have full X inactivation

I think that they mean the first, actually, but I would aim to seek clarification from the authors