User: khn

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khn110
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Posts by khn

<prev • 67 results • page 1 of 7 • next >
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Many mismatch allele for meta analysis by plink
... Hello, I am doing meta analysis by plink. Given many allele mismatch, no SNPs in ChrX remained after meta analysis, though it went well for Chr1-22. I figured out that the issues are flip. I do not think it is correct just to flip A1 and A2 for SNPs in ChrX in one summary statistics, and do meta a ...
genome gene snp written 9 weeks ago by khn110
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FINEMAP - output files
... Hello, Is anybody familiar with FINEMAP? There are some output files but it is a little complicated to interpret and be used for further analysis. I want to draw locus zoom, using the output files from the FINEMAP. One of the output files is SNP file, which includes the data of log 10 bays and p ...
gene snp written 8 months ago by khn110 • updated 6 months ago by christian.benner20
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How to calculate frequencies of SNPs after meta-analysis by plink?
... Hello, Do you know how to calculate frequencies of SNPs after meta-analysis by plink? Summary stats that the plink produces do not include frequency of SNPs. So, how do you calculate it? Or do you just start using METAL as the information from plink is so limited by meta-analysis? Thank you in adv ...
genome tool snp sequencing written 8 months ago by khn110 • updated 8 months ago by Nicolas Rosewick9.3k
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Answer: A: Meta analysis by plink
... I think I figured out the answer - if we want to use BETA as a effect size, we must add +logscale in the code... ...
written 9 months ago by khn110
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Meta analysis by plink
... Hello all, I am conducting meta-analysis by plink. I created two files, following the website of plink. The headers for the two files are CHR BP A1 A2 SNP BETA SE P. I ran --meta-analysis but the error message shows "no effect sizes are found". I just changed only the header from BETA to OR, and it ...
genome tool snp written 9 months ago by khn110
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Adding dosage for a SNP as a covariate to a phenotype file
... Hello I want to add a SNP information to a phenotype file, in addition to sex, age and PC 1~10. Does anybody know how to do it? I think I need to retrieve dosage information from vcf.gz file first, then retrieve dosage information only for the SNP. Is this how you guys usually do? Thank you in adv ...
genome gene snp written 9 months ago by khn110 • updated 9 months ago by Lemire600
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low genomic inflation factor
... Hello I usually adjust MAF if the genomic inflation factor is too low. But how low could be still acceptable? I know that the maximum number could be 1.10, but how about the minimum? Thank you! ...
genome snp sequencing written 10 months ago by khn110
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Answer: A: To keep the model of minimum p-value from the file
... tail -n +2 original_file > txt sort -t, -k 4g txt | awk -F, '!visited[$1]++' | sort -k2,2 -k3,3 >> final_file ...
written 11 months ago by khn110 • updated 11 months ago by zx87549.9k
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Comment: C: To keep the model of minimum p-value from the file
... Thank you for your comment. I just wanted to draw a manhattan plot based on this. But I think I should just show three manhattan plots, based on the model. ...
written 12 months ago by khn110
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To keep the model of minimum p-value from the file
... Hello My file lists a millions of SNPs with their p-values by additive, dominant, and recessive models. I want to keep the SNPs with a model for which the p-value is the lowest. Original file.txt ID,y,z,P-value rs1,a,b,0.22 rs1,a,b,0.35 rs1,a,b,0.45 rs2,c,d,0.06 rs2,c,d,0. ...
gene snp written 12 months ago by khn110

Latest awards to khn

Great Question 7 months ago, created a question with more than 5,000 views. For Merging bed bim fam files from chromosome 1 to 22 at one time
Popular Question 7 months ago, created a question with more than 1,000 views. For Sample size calculation for GWAS (fixed number of controls)
Popular Question 7 months ago, created a question with more than 1,000 views. For Plink-handling multiallelic variant to merge two datasets
Popular Question 7 months ago, created a question with more than 1,000 views. For Inflated qq plot and genomic inflation est. lambda
Popular Question 8 months ago, created a question with more than 1,000 views. For How to merge two dosage files?
Popular Question 9 months ago, created a question with more than 1,000 views. For Binary to DNA sequence
Supporter 10 months ago, voted at least 25 times.
Popular Question 11 months ago, created a question with more than 1,000 views. For Binary to DNA sequence
Popular Question 14 months ago, created a question with more than 1,000 views. For Plink-handling multiallelic variant to merge two datasets
Popular Question 22 months ago, created a question with more than 1,000 views. For Merging bed bim fam files from chromosome 1 to 22 at one time
Popular Question 24 months ago, created a question with more than 1,000 views. For Plink-handling multiallelic variant to merge two datasets
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Binary to DNA sequence

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