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KosukeHamazaki / RAINBOWR

Reliable Association INference By Optimizing Weights with R (R package for SNP-set GWAS and multi-kernel mixed model)
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007663
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When performing SNP-set GWAS, the wrong genotype data was incorrect, but my data format was encoded as -1.0, 1 #10

Open youziy123456 opened 4 months ago

youziy123456 commented 4 months ago

Error in calcGRM(genoMat = Mis, methodGRM = "addNOIA", returnWMat = TRUE, : Genotype data should be scored with (-1, 0, 1) or (0, 1, 2)!!

KosukeHamazaki commented 4 months ago

Dear youziy123456,

Thank you for your contact. I'm sorry for the inconvenience, but I cannot the reason without checking your data. If you can, please share the results of table function applied to your dataset. Also, please check whether your data includes the missing data.

Best regards, Kosuke

youziy123456 commented 4 months ago

Hello, here are my genos.txt, map.txt and pheno.txt. data.docx Thank you for your reply.

KosukeHamazaki commented 4 months ago

Thank you for your data. It seems that you could compute the genome-wide global relationship matrix, but you failed to compute the local relationship matrix. Please check you performed the SNP filtering with MAF.cut function.

Also, if you can share marker genotype data of the first 1000 markers, it will help to solve the problem.

youziy123456 commented 4 months ago

Hello, Yes, I performed the SNP filtering with MAF.cut function. Below is the marker genotype data for my first 1000 markers genotype2.txt

KosukeHamazaki commented 4 months ago

Hi,

Thank you for sharing your data. I fixed the error and updated the RAINBOWR to version 0.1.36. Please install the latest version via GitHub and check if your code works.

Best regards, Kosuke

youziy123456 commented 4 months ago

Thank you for your prompt response, which I greatly appreciate.