error in pullSnpGeno() function

[Anilkumargpb]

HI everyone,

I was generating the founder population, including marker data, marker effects, and map information, with following codes. after a round of random crossing, the snp information of simulated population is showing zeros for all markers upon pulling snp genotypes. Here are the codes used.
founderPop=importInbredGeno(geno = snp, genMap = GenMap, ped = NULL)
SP = SimParam$new(founderPop)
SP$importTrait(markerNames = qtlEffects$marker,
addEff = qtlEffects$aditiveEffect,
name = "Your_Trait")
SP$addSnpChip(5)
Parents = newPop(founderPop)
F1 = randCross(Parents, 200)
HDRW = makeDH(F1, 100)
pullSnpGeno(HDRW)

Let me know where I am going wrong.

Thanks

[gregorgorjanc]

@Anilkumargpb makeDH() is creating doubled-haploid (DH) (=fully homozygous) individuals, so genotypes of all 0s makes sense, but seeing just 0s is troubling - we would expect homozygous 0 and 2 - at least in some proportion. Maybe you are only looking at some individuals and some markers? Or is your snp genotype matrix really sufficiently diverse?

What do these commands report:

• table(c(pullSnpGeno(HDRW))) # trying to see distribution of 0s and 2s
• colMeans(pullSnpGeno(HDRW)) / 2 # trying to see allele freqs at markers

[Anilkumargpb]

HI Gregor

Thanks for the detailed information. I found my mistake, it was due to a set of markers that are not polymorphic.

Thanks

[Anilkumargpb]

Hi

I have a question on the same topic, when I am using pullSnpGeno(HDRW) its only giving information on a set of SNPs. How do I pull information of all markers?
Please let me know.

Thanks

[gaynorr]

The function pullSegSiteGeno will give you the genotype information for all the markers.

The pullSnpGeno function is designed to extract a subset of markers that have been assigned to a SNP chip. The function pullMarkerGeno will give you genotype information for specific markers you request.

[Anilkumargpb]

Thank you so much Chris