I created raw file from map and ped file and then did some LD pruning. On these pruned SNPs, run the analysis and now get the final results with few SNPs in the form of Raw file . Now I want to go back to get the partner SNPs of my analyzed SNPs from the Pruned out file and combined them. Is it possible in Plink or Rstudio? and secondly I have Raw file and I am unable to convert it back to Ped or map file. Please tell me the commands?

Thank you.

Jawad