converting .txt file to .ped and .map files

Question

[jyothisrilok]

Hello everyone,

I have a .txt with columns - CHR , SNPID , Position, P value , TA, OA , Frequency , Beta, SE and N.

My goal is to perform LD clumping. I tried LDLinkR package which has not been an efficient method since I had nearly 41,000 SNPs. Please advise how I may convert the .txt file into .ped and .map files to use PLINK for LD clumping.

Thank you for your help.

Answer 1

[Hirofumi]

Hello jyothisrilok,
PLINK format files consist of individual Genotype data.
Since they cannot be converted from summary data, please consider other methods aside from converting to PLINK format.

[Hirofumi]

Consider the following alternative methods:

1. Perform approximate LD pruning using a reference panel dataset, such as the 1000 Genomes Project. However, caution is needed in the choice of data populations.

2. Obtain actual sample genotype data.

[jyothisrilok]

Thank you so much Hirofumi. I am quite new to GWAS studies and this helped me understand how different are summary stats from the genotype data. I used LD_clumping in R and it worked. Thank you.