Warning running assoc.map

[Rhodnius]

Hello,

I am having a warning and I don't know if that are altering the results I am having

I am running this function:

assoc.map( pheno = pheno, pheno.col = c(5), probs = model.probs6, K = K3, addcovar = covar, snps = muga_snps, chr = 15,

chr = interval[1, 2], # here you can call values in interval

start = interval[1, 3],

end = interval[3, 3]

start = 74.000, # or you can insert only the values here end = 78.000 # ideally these regions are the regions where the QTLS are located )

This generates this warning:

Warning message:

In .vcf_map_samples(samples(hdr), samples) : samples not in file: ‘C57BL_6J’

Do you know what does it means?

Thanks a lot.

The session info is: sessioninfo_020920.txt

[gboysen]

I am not sure but you have to fix C57BL_6J to C57BL/6J or similar i check later. Check your names

Sent from my iPhone

On Mar 9, 2020, at 3:14 PM, Rhodnius notifications@github.com wrote:

C57BL_6J

[ytakemon]

The founders are usually named A:H, with C57BL/6J being B (see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4602074/figure/Fig1/). You might want to check how your founder alleles are being named in your probs file and across your files.

[ytakemon]

Also, many of us have moved to qtl2 (https://kbroman.org/qtl2/) for DO QTL analyses. qtl2 is actively maintained by Karl and has some nice additional features that you might want to consider. Good luck.

[Rhodnius]

Also, many of us have moved to qtl2 (https://kbroman.org/qtl2/) for DO QTL analyses. qtl2 is actively maintained by Karl and has some nice additional features that you might want to consider. Good luck.

Thanks for the suggestion, Yuka!

Indeed, I have been using qtl2, and I love its plasticity. But, I had some problems finding some funnel codes (similar to those found in Srivastava et al. 2017, SupTabl2) and the absence of some genotypes for some CCs, mainly from CC079-CC084.

Currently, I am using DOQTL because of the model.probs default from DOQTL. With this information, I could quickly generate the association plots (that I never could generate in qtl2).

I also compared the results that I was generating between qtl2 and DOQTL, and they were not the same.

So, for instance, I will run the analysis in parallel in qtl2 and DOQTL...

Best,

Juan C.

[Rhodnius]

The founders are usually named A:H, with C57BL/6J being B (see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4602074/figure/Fig1/). You might want to check how your founder alleles are being named in your probs file and across your files.

That's the thing... My probs file only has A:H names, and I am not using in DOQTL other files with the full names of the parentals, so I have no idea...

Thanks for the suggestion, though!