User: analyticalavailable

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Ireland
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5 years, 7 months ago
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5 years, 10 months ago
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Posts by analyticalavailable

<prev • 19 results • page 1 of 2 • next >
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Comment: C: How to calculate the increase in qualitative disease score per risk allele?
... Running both the lm and gam, I find that I am not getting the results that I need from the summary/anova. (per G allele IRR 0.89, 95% confidence interval [95% CI] 0.82, 0.97; PLR  0.002) So, in my case I should be seeing a percentage lower risk of the disease for AA over GA and GG. So in the abo ...
written 5.6 years ago by analyticalavailable30
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Comment: C: How to calculate r-squared with Haploview from different sources?
... Someone mentioned to me that I could output each of the SNPs into an excel file, and do it from there. Then I would need a file with the pair of genotypes at each locus listed for each person. I'm actually a computer scientist, I've never used this tool before. Are we talking two columns, with each ...
written 5.6 years ago by analyticalavailable30
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Comment: C: How to calculate r-squared with Haploview from different sources?
... Yes, ~97% of them. ...
written 5.6 years ago by analyticalavailable30
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How to calculate r-squared with Haploview from different sources?
... I would like to get the r-squared for two SNPs in my population. One of the SNPs is in a mySQL db, and the other is currently also in a mySQL db, but I have the plink files for that one. Can anyone advise me on how I will go about getting these into a format that Haploview will understand? EDIT: ...
snps plink haploview written 5.6 years ago by analyticalavailable30 • updated 5.6 years ago by zx87549.6k
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Comment: C: How to calculate the increase in qualitative disease score per risk allele?
... I actually prefer R, so thank you very much for this. I believe that it is the additive model that I am looking for right now, since I would like to see what the interaction with the homozygous A. Would you be able to suggest the function/library that is used to do that kind of analysis? Data is c ...
written 5.6 years ago by analyticalavailable30
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Comment: C: How to calculate the increase in qualitative disease score per risk allele?
... OK, I'm kind of new to this area so I am coming in a little blind. I've the score that varies between 0-100, for 1000 people. For each of those, I've the GG (most common homozygote) as 0, GA as 1 and AA (least common homozygote). What I am gathering from online is that I need to break each genotype ...
written 5.6 years ago by analyticalavailable30
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How to calculate the increase in qualitative disease score per risk allele?
... Hi, I'd like to calculate the increase in qualitative disease score per risk allele. I've a cohort of 1000, and a single SNP, for each of the individuals, I've a score from 0 to 100. It was recommended that I use a linear regression model. Can anyone elaborate on why you might use a linear regress ...
R snp written 5.6 years ago by analyticalavailable30 • updated 5.6 years ago by Devon Ryan96k
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Comment: C: Unknown output in .ped with plink2 --extract
... Thanks. When performing a GWAS, how are such insertions usually treated? ...
written 5.7 years ago by analyticalavailable30
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Comment: C: Unknown output in .ped with plink2 --extract
... Can you explain what insertion means in this case? I'm computer science, and new to this. Cheers. ...
written 5.7 years ago by analyticalavailable30
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Unknown output in .ped with plink2 --extract
... I'm trying to extract the alleles for each of the SNPs in a dataset I have, using the following plink2 command. ./plink2 --bfile chr1 --recode --extract snp.dat --out snp --noweb I find that instead of two alleles for each subject, I have more than one e.g. "TC". 75 VS9 0 0 1 -9 T T 76 VS7 0 0 2 ...
plink2 snp written 5.7 years ago by analyticalavailable30 • updated 5.5 years ago by Biostar ♦♦ 20

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