User: Agatha

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Agatha340
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5 years, 10 months ago
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8 years, 3 months ago
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bioinformatics student :-)

Posts by Agatha

<prev • 77 results • page 1 of 8 • next >
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Comment: C: Ldheatmap Does Not Include All Snps In The Analysis (Tri-Allelic Snp Excluded)
... that's probably it...thought so as well. thanks for the alternative suggestions. ...
written 6.1 years ago by Agatha340
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Comment: C: Plink Snp- Quantitative Trait Association - P-Value Is 0
... That must be the case ... I have looked in the documentation, forums, examples but I couldn't find anything similar to what I have or any information about the thresholds... ...
written 6.1 years ago by Agatha340
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Plink Snp- Quantitative Trait Association - P-Value Is 0
... I have run PLINK --assoc for a list of snps and the associated genotypes and qt measurements. The SNP I have added as control (control= it is known that it is highly associated with the analyzed quantitative trait ) is returned as having a p-value of 0. When doing a separate linear regression an ...
plink written 6.1 years ago by Agatha340 • updated 6.1 years ago by Drei50
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Ldheatmap Does Not Include All Snps In The Analysis (Tri-Allelic Snp Excluded)
... I am trying to generate an LD plot using LDheatmap in R. I have 4 SNPs geotyped for around 80 000 individuals : head(m.genos) p1205 p0864 p3077 p1244 1 G/G C/C T/T C/C 2 A/A C/C T/T C/C 3 G/G T/T T/T T/T 4 A/A C/C T/T C/C 5 G ...
R snp written 6.1 years ago by Agatha340 • updated 6.1 years ago by Fabio Marroni2.3k
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Comment: C: Large Significance Difference In Association Analysis For Quality Control Snps (
... @zx8754 - 4. population size >8000 2. no mixup 3. there is a small difference between the MAF values and genotype counts ...
written 6.4 years ago by Agatha340
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Comment: C: Large Significance Difference In Association Analysis For Quality Control Snps (
... Yes, I have. Total amount of missing genotypes for all considered snps is lower than 0.2% ...
written 6.4 years ago by Agatha340
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Comment: C: Snp - Quantitative Trait Association In A Gwa Study
... I have tried using plink for this , --assoc option , but I have only got the basic snp-qt association results. I have probably done something wrong when using --gxe returned only NA values...although I think I have used the correct input formats .. ...
written 6.4 years ago by Agatha340
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Snp - Quantitative Trait Association In A Gwa Study
... I have a list of 700 snps and the associated genotypes for 8500 individuals. I am trying to analyze the association between the SNPs and two quantitative traits. ( => which snp is associated the most with each one of them). I was considering to generate a linear regression model with each of th ...
gwas snp written 6.4 years ago by Agatha340 • updated 6.2 years ago by yao.h.19880
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Comment: C: Obtaining Ld Values For A Snp Against All Others Within A Defined Region Using
... Exactly what I needed. Thanks a lot. ...
written 6.5 years ago by Agatha340
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Comment: C: Obtaining Ld Values For A Snp Against All Others Within A Defined Region Using
... Yes it's there..thanks. However i have checked the Biomart API and there is not way to get the information automatically, is it - for a higher number of snps? ...
written 6.5 years ago by Agatha340

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