11 weeks ago by
How many chromosomes does your species have? Also, are all chromosomes
diploid for all individuals? The reason assocTestMM wants sex is so that
chromosome 23 (which typically represents the X chromosome in humans) can
be coded correctly for males vs. females. If all of your individuals are
diploid at all chromosomes, then the easiest thing might be to make a fake
sex column in your scanAnnot that says 'F' for everyone.
Let me know if you have further questions.
On Tue, Jul 24, 2018 at 7:59 PM, naglemi [bioc] <email@example.com>
> Activity on a post you are following on support.bioconductor.org
> User naglemi <https: support.bioconductor.org="" u="" 16588=""/> wrote Question:
> GENESIS: assocTestMM error for lack of sex chromosome info (not relevant
> for this species) <https: support.bioconductor.org="" p="" 111361=""/>:
> I'm working with a species that does not have sex chromosomes. The only
> part of the workflow in which I see I can note this is while building the
> GRM – by setting the option autosome.only to TRUE. I've looked through R
> documentation for assoctestMM and don't see a way to specify that there are
> no sex chromosomes in this dataset. How can I do this? Thanks for your time.
> Here are relevant lines prior to the line causing the error, showing how I
> specify autosome-only to be TRUE:
> grm <- snpgdsGRM(genofile, sample.id=keep, snp.id=NULL, autosome.only=TRUE, remove.monosnp=TRUE, maf=.05, missing.rate=.05, method="GCTA", num.thread=1L, with.id=TRUE, verbose=TRUE)
> LMMnullmod=fitNullMM(scanData=scanAnnotTRANS,outcome="SW3_TDZ",covMatList=GRM, family=gaussian)
> Here is the line that causes the errror, and the error:
> > assoc <- assocTestMM(genoData = genoData, nullMMobj = LMMnullmod, test = "Wald")
> Error in assocTestMM(genoData = genoData, nullMMobj = LMMnullmod, test = "Wald") :
> Sex values for the samples are required to compute MAF for X chromosome SNPs
> Post tags: GENESIS, assoctestmm, GWAS
> You may reply via email or visit https://support.bioconductor.
Matthew P. Conomos, PhD.
Department of Biostatistics Genetics Analysis Center
University of Washington
Seattle, WA 98105-1016, USA
phone: (206) 685-8848