Question: PLINK: How to concatenate PED and MAP files into single data-frame?
gravatar for reza.jabal
3.0 years ago by
United Kingdom
reza.jabal320 wrote:

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.

plink modelling python • 1.5k views
ADD COMMENTlink modified 3.0 years ago by Joey410 • written 3.0 years ago by reza.jabal320
gravatar for Joey
3.0 years ago by
Joey410 wrote:

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
ADD COMMENTlink written 3.0 years ago by Joey410
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 799 users visited in the last hour