User: fatima

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fatima10
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Posts by fatima

<prev • 15 results • page 1 of 2 • next >
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Comment: C: error in merging data by two versions of plink
... It means you should use bed file at first and bim and fam respectively (exactly in the same order is written in plink instructure). ...
written 2.3 years ago by fatima10
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The interpretation of OR and p-value in plink.assoc
... Dear all, I did association test by --assoc in plink. What is the exact interpretation of OR, p-value and chi-square test in this file? I know the definition of all concepts but what does it mean in this file? For example, what is the relation of significant p-value with chi-square test and OR? Th ...
p-value odds ratio plink association test written 2.4 years ago by fatima10
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result of imputation is vice versa
... Dear all, I impute some SNP that I have their real genotype by minimac3. I checked strand alignment and remove problematic SNPs and phased them by shapit. the result of imputation for rs... is AG , but the reall genotype in my data set is GA, or for another one imputed SNPs is CT but the real one ...
shapeit imputation minimac3 genotype plink written 2.4 years ago by fatima10
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Negative and positive linkage disequilibrium
... Hello everyone, Could you explain me what is exactly the meaning of Negative and positive LD which mentioned in Plink "-flip-scan"? The result fo the "--flip-scan" is plink.fipscan and I have nan for all elements of R_NEG column. What is the problem for that? Thank you. ...
linkage gwas plink ld written 2.4 years ago by fatima10 • updated 13 months ago by seta1.1k
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Comment: C: error in merging data by two versions of plink
... I found the problem. The order in bed, bim and fam file is important. ...
written 2.4 years ago by fatima10
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error in merging data by two versions of plink
... Dear all, **I tried to merge two binary file(my data set and the reference panel 1000G), but I get just fam file and log file** : Options in effect: --bfile mydata --bmerge ref.bim ref.bed ref.fam --make-bed --out mergefiles Reading map (extended format) from [ mydata.bim ] 17838 markers t ...
plink bmerge written 2.4 years ago by fatima10
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Comment: C: Selecting Specific Snps An Imputed Genotype File
... Could you find the solution? I have imputaed SNPs file in Minimac3 and I'd like to extract a especial set of imputed SNPs. Which software or method you used? Thank you. ...
written 2.4 years ago by fatima10
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Comment: C: Step by step instructions to phase with Eagle?
... sorry, I found the problem! ...
written 2.5 years ago by fatima10
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How to check consistency of data sets and 1000G reference panel?
... Hi everyone, I have a set of data including cases in plink format and the genotypes come from immunochip. To start prephasing the data I would like to check if they are in the same build(my reference panel is 1000G build 37,phase 3 . How I can do that? If comparing the map files is a good way? Th ...
map file immunochip build written 2.5 years ago by fatima10
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what is the reason for having different phenotypes and snps?
... Hi everyone, I have a question.I have a set of data including cases in plink format. some SNPs have "I" or "D" phenotype instead of A,T,C,G!! What is the reason for that? Can they be the reason for having Triallelic error in merging two data set? In addition some SNPs do not start by rs.... , for ...
triallelic different snps plink written 2.5 years ago by fatima10

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