User: rkl

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rkl0
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Posts by rkl

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Linkage disequilibrium clumping in plink
... Hi, Sorry if this is a silly question. I created a polygenic risk score for a disease. As a sensitivity analysis, I removed SNPs associated with education and reclumped the SNPs. Now, I get more SNPs in the .bim file with the clumped SNPs(without education) than the original anlaysis even though I ...
ld clumping plink written 5 months ago by rkl0
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Check whether two GWAS are from the same ancestry
... Hi all, I've performed a meta-analysis and want a way of seeing whether the people in my GWAS all have European ancestry by checking the allele frequency compared to 1000G. Is there any program that can check for differences for large datasets? Thanks ...
allele frequency written 6 months ago by rkl0 • updated 6 months ago by Kevin Blighe46k
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PLINK meta-analysis when there is SNP for just one study
... Hi, I am encountering an issue with my meta-analysis. Although, plink reads all 3 studies, when there is 1 study it outputs NA for the betas, SEs and associated values even though I specify for it to report all --meta-analysis SP_reformatted.assoc GC_reformatted.assoc AP_reformatted.assoc + qt ...
plink written 7 months ago by rkl0 • updated 7 months ago by zx87547.9k
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BOLT LMM - invalid heritability estimate error
... Hi, I am trying to perform a GWAS for a variable. There is not a huge sample for it and BOLT-LMM says that the heritability estimate is invalid. I was wondering what exactly does this mean? Is it an error that can't be fixed or is it a technical error that I can fix? Thanks in advance ...
genome snp written 7 months ago by rkl0
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How to incorporate interaction between two alleles in ApoE for Alzheimer's polygenic risk score?
... Hi, I am generating a polygenic risk score for Alzheimer's disease and want to include ApoE. However, I'm not sure how I'd include the interaction between these alleles in the PRS. For example, I include the two SNPs tagging the locus rs7412 and rs429358 with the effects provided by IGAP. However, ...
snp written 8 months ago by rkl0 • updated 7 months ago by Biostar ♦♦ 20
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Comment: C: Meta-analysis in PLINK - What to use in order to do a forest plot
... Hi, Don't know if it's the right place but how did you convert the plink output (plink.meta) file into a format readable by R. Thought I'd ask here as you seem to have done a meta-analysis. Thanks ...
written 8 months ago by rkl0
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Comment: C: Meta-analysis in PLINK - What to use in order to do a forest plot
... Hi, Don't know if it's the right place but how did you convert the plink output (plink.meta) file into a format readable by R. Thought I'd ask here as you seem to have done a meta-analysis. Thanks ...
written 8 months ago by rkl0
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Comment: C: How to convert a meta-analysis file from PLINK (.meta) to a .csv or.txt to be re
... its the default output of plink meta-analysis which is plink.meta (text file). When I try to import it into R it can't differentiate the columns. CHR BP SNP A1 A2 N P P(R) BETA BETA(R) Q I 1 751343 rs28544273 T A ...
written 8 months ago by rkl0 • updated 8 months ago by WouterDeCoster40k
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How to convert a meta-analysis file from PLINK (.meta) to a .csv or.txt to be read into R?
... Hi, I'm encountering issues with reading .meta files into R. I am assuming the file needs to be reformatted to a .csv or a .txt. Does anyone have any idea of how to convert the PLINK output for meta-analysis (plink.meta) to a file format readable by R? Thanks! ...
R plink written 8 months ago by rkl0 • updated 8 months ago by zx87547.9k
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Comment: A: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
... Hi Kevin, Does the following command do a liftover of 1000 genomes to Hg19. I need to do QC on 1000 genomes data before using for LD clumping and as I haven't done this before, I'm a bit unsure. I followed your steps until this point and then proceeded to convert to plink, removed SNPs based on ca ...
written 9 months ago by rkl0

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