User: khn
khn • 110
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Posts by khn
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... 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 ...
written 9 weeks ago by
khn • 110
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... 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 ...
written 8 months ago by
khn • 110
• updated
6 months ago by
christian.benner • 20
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... 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 ...
written 8 months ago by
khn • 110
• updated
8 months ago by
Nicolas Rosewick ♦ 9.3k
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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
khn • 110
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... 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 ...
written 9 months ago by
khn • 110
1
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... 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 ...
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... 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! ...
written 10 months ago by
khn • 110
0
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... tail -n +2 original_file > txt sort -t, -k 4g txt | awk -F, '!visited[$1]++' | sort -k2,2 -k3,3 >> final_file ...
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... 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
khn • 110
3
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... 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. ...
written 12 months ago by
khn • 110
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