User: kumar.vinod81

gravatar for kumar.vinod81
kumar.vinod81280
Reputation:
280
Status:
Trusted
Location:
New Delhi
Last seen:
5 months ago
Joined:
6 years, 6 months ago
Email:
k************@gmail.com

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

Posts by kumar.vinod81

<prev • 104 results • page 1 of 11 • next >
0
votes
1
answer
2.8k
views
1
answers
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 5 months ago by kumar.vinod81280
0
votes
0
answers
140
views
0
answers
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 5 months ago by kumar.vinod81280
0
votes
1
answer
2.8k
views
1
answers
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 5 months ago by kumar.vinod81280
0
votes
1
answer
315
views
1
answers
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 8 months ago by kumar.vinod81280
0
votes
0
answers
143
views
0
answers
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 8 months ago by kumar.vinod81280
1
vote
0
answers
910
views
0
answers
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 2.7 years ago by kumar.vinod81280
1
vote
0
answers
970
views
0
answers
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 2.8 years ago by kumar.vinod81280
0
votes
0
answers
1.1k
views
0
answers
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 2.9 years ago by kumar.vinod81280
0
votes
1
answer
1.4k
views
1
answers
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 2.9 years ago by kumar.vinod81280
0
votes
1
answer
1.4k
views
1
answer
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 2.9 years ago by kumar.vinod81280 • updated 2.9 years ago by Floris Brenk880

Latest awards to kumar.vinod81

Popular Question 5 months ago, created a question with more than 1,000 views. For Snp Information From Ped File In Plink
Popular Question 8 months ago, created a question with more than 1,000 views. For Snp Information From Ped File In Plink
Popular Question 12 months ago, created a question with more than 1,000 views. For Snp Information From Ped File In Plink
Popular Question 12 months ago, created a question with more than 1,000 views. For haplotype association with quantitative traits
Great Question 16 months ago, created a question with more than 5,000 views. For Phenotypic Variation Explained By Snps In Gwas
Popular Question 16 months ago, created a question with more than 1,000 views. For Snp Information From Ped File In Plink
Popular Question 16 months ago, created a question with more than 1,000 views. For Transpose large excel data containing thousands of rows
Popular Question 16 months ago, created a question with more than 1,000 views. For fastPHASE output format to PLINK input format
Popular Question 16 months ago, created a question with more than 1,000 views. For Association Mapping: Can Mlm Find More Association Than Glm?
Popular Question 16 months ago, created a question with more than 1,000 views. For What Is Haplotyping In Context Of Gwas?
Popular Question 16 months ago, created a question with more than 1,000 views. For Need Recommendation On Good Tutorials For Performing Gwas
Popular Question 19 months ago, created a question with more than 1,000 views. For Snp Information From Ped File In Plink
Popular Question 19 months ago, created a question with more than 1,000 views. For Association Mapping: Can Mlm Find More Association Than Glm?
Popular Question 19 months ago, created a question with more than 1,000 views. For fastPHASE output format to PLINK input format
Popular Question 19 months ago, created a question with more than 1,000 views. For Need Recommendation On Good Tutorials For Performing Gwas
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Snp Information From Ped File In Plink
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Snp Information From Ped File In Plink
Appreciated 2.6 years ago, created a post with more than 5 votes. For Need Recommendation On Good Tutorials For Performing Gwas
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Snp Information From Ped File In Plink
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Snp Information From Ped File In Plink
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Snp Information From Ped File In Plink
Centurion 2.9 years ago, created 100 posts.
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Does Imputation Always Need Reference Panel
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Need Recommendation On Good Tutorials For Performing Gwas

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1173 users visited in the last hour