User: kumar.vinod81

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kumar.vinod81280
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I am M.Sc., Ph.D. in plant biotechnology

Posts by kumar.vinod81

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Comment: C: Phenotypic Variation Explained By Snps In Gwas
... 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.vinod81280
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phenotypic variance explained by non-additive model in GenABEL
... 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 ...
gwas non-additive model written 9 weeks ago by kumar.vinod81280
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Comment: C: Phenotypic Variation Explained By Snps In Gwas
... 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.vinod81280
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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.vinod81280
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VIFGC_ovedom function in GenABEL
... 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 ...
genabel non-additive models written 5 months ago by kumar.vinod81280
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Simulation in quantitative genetics, mapping and gwas
... 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 ...
gwas simulation written 2.5 years ago by kumar.vinod81280
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Boxplot of phenotype~SNP1:SNP2
... ![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 ...
boxplot snp written 2.5 years ago by kumar.vinod81280
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Interpretation for regression coeffecient and T statistics from haplotype association in PLINK
... 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 ...
haplotype association written 2.6 years ago by kumar.vinod81280
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Comment: C: haplotype association with quantitative traits
... 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.vinod81280
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haplotype association with quantitative traits
... 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? ...
gwas haplotype written 2.7 years ago by kumar.vinod81280 • updated 2.7 years ago by Floris Brenk860

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Popular Question 8 weeks ago, created a question with more than 1,000 views. For Snp Information From Ped File In Plink
Popular Question 5 months ago, created a question with more than 1,000 views. For Snp Information From Ped File In Plink
Popular Question 9 months ago, created a question with more than 1,000 views. For Snp Information From Ped File In Plink
Popular Question 9 months ago, created a question with more than 1,000 views. For haplotype association with quantitative traits
Great Question 13 months ago, created a question with more than 5,000 views. For Phenotypic Variation Explained By Snps In Gwas
Popular Question 13 months ago, created a question with more than 1,000 views. For Snp Information From Ped File In Plink
Popular Question 13 months ago, created a question with more than 1,000 views. For Transpose large excel data containing thousands of rows
Popular Question 13 months ago, created a question with more than 1,000 views. For fastPHASE output format to PLINK input format
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Popular Question 13 months ago, created a question with more than 1,000 views. For What Is Haplotyping In Context Of Gwas?
Popular Question 13 months ago, created a question with more than 1,000 views. For Need Recommendation On Good Tutorials For Performing Gwas
Popular Question 16 months ago, created a question with more than 1,000 views. For Snp Information From Ped File In Plink
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Popular Question 16 months ago, created a question with more than 1,000 views. For fastPHASE output format to PLINK input format
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Popular Question 2.5 years ago, created a question with more than 1,000 views. For Snp Information From Ped File In Plink
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Snp Information From Ped File In Plink
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