User: kumar.vinod81
kumar.vinod81 • 280
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I am M.Sc., Ph.D. in plant biotechnology
Posts by kumar.vinod81
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... Really didn't understand, exactly what you want to do? In GenABEL, its really tough to get r2 directly. You can follow this link http://forum.genabel.org/search.php?keywords=phenotypic+variance+explained+by+SNP for more clarity. Or you can deleted the most significant SNP and then see the difference ...
written 9 weeks ago by
kumar.vinod81 • 280
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... I am using non-additive GWAS models implemented in GenABEL. mlreg model was used to find out dominant, recessive and over-dominance SNP effect and test statistics was corrected using VIFGC function for non-additive models. How to calculate heritability explained by the significant SNP and whole data ...
written 9 weeks ago by
kumar.vinod81 • 280
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... you can fit multiple linear regression in R by fitting all the significant SNPs (vector in R) as explanatory variable while the trait of interest (vector in R) as a response variable. ...
written 9 weeks ago by
kumar.vinod81 • 280
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Answer:
A: recode SNPs ATGC illumina
... Export file in PLINK format and you will find a lot of options in PLINK for genotypes recoding. ...
written 5 months ago by
kumar.vinod81 • 280
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... I am using non-additive functions implemented in GenABEL. VIFGC function for dominant and recessive non-additive model is working fine but with the same data, VIFGC_ovedom function is giving an error:
Error: Error in nlm(GC_VIF_nlm, c(F = F1, K = K1)) : missing value in parameter
Also, how to calcu ...
written 5 months ago by
kumar.vinod81 • 280
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... Could anybody suggest me about the literature on Simulation in quantitative genetics and gwas ? I am a wet lab student and not much aware with this term but I've listen this word so many time and in so many research papers as I am working on GWAS but I am not able to find papers regarding its real m ...
written 2.5 years ago by
kumar.vinod81 • 280
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... ![enter image description here][1]Can I generate a boxplot like the one attached in image ?
I just know simple one.
boxplot(phenotype~SNP1:SNP2)
![boxplot like this][1]
[1]: https://s26.postimg.org/447qeuhm1/boxplot.jpg ...
written 2.5 years ago by
kumar.vinod81 • 280
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... I have generated haplotype block of a chromosomal region and used it for hap association of quantitative trait in plink. I am ok with R2 and P-val but not with regression coeffecient and t statistics. I am getting two haplotype significantly associated but one with positive and one with negative Reg ...
written 2.6 years ago by
kumar.vinod81 • 280
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... Thanks Floris,
But I am not able to use --blocks output as myfile.hlist as both are quite different. Do you have any idea?
thanks for your help ...
written 2.7 years ago by
kumar.vinod81 • 280
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... I have a done a GWAS study in plant for quantitative trait and found some regions higly significant. Now, I want to see the haplotye structure around these SNPs and their reassociation with the trait so, I can capture the contributing haplotype. Does anyone know any tool which can make it possible?
...
written 2.7 years ago by
kumar.vinod81 • 280
• updated
2.7 years ago by
Floris Brenk • 860
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