PLINK: How to concatenate PED and MAP files into single data-frame?

Question

[reza.jabal]

Hi Everyone, I am trying to build a random forest classifier for a 6K microarray data. Preliminary analysis is carried out in plink and respective bed/bim/fam files are passed to me for additional analysis. As I am modeling the data in Python, I require to concatenate those files into one single data-frame which I could pass it to python. I am wondering if there's any way I could merge PED & MAP files. I would like to keep individual's ID and their genotype/phenotype data.

Answer 1

[Joey]

Look at the --recodeA option in PLINK v1.07 or --recode A option in PLINK v1.90. It might be what you want.

Say you have example.fam, example.bim, example.bed something like

plink --bfile example --recodeA --out recoded