User: rkl

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rkl0
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Posts by rkl

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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 days 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 9 days 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 9 days 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 9 days ago by rkl0 • updated 9 days ago by WouterDeCoster35k
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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 9 days ago by rkl0 • updated 8 days ago by zx87546.1k
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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 6 weeks ago by rkl0

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