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

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

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

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 python modelling

• 4,094 views • link

updated 10.3 years ago by Joey

• written 10.3 years ago by reza.jabal

1 answer

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

• 1 views • link

written 10.3 years ago by Joey

Log in to answer this question.

More posts like this

genome data size
written 2.5 years ago by kkk •

Hello I need to know the data size of genome data. I know it depends on the analysis, but is there a site that can …
Differences between BED and bed files
written 3.7 years ago by naz •

Hello, I am very new to bioinformatics and I apologize if this question is simple/obvious. My goal is to perform a polygenic risk score analysis …
DGRP data set
written 7.3 years ago by mvanligten14 •

Hi, I am currently in the process of trying to find mutually exclusive SNPs in a subset of the dgrp data. I was able to …
Merge ped files in PLINK
written 9.5 years ago by AR3513 •

Hi, I'm very new using PLINK. I have two data sets of SNP data and both data sets contain .ped, .bim, .fam files. I would …
plink 1.9 PED to VCF, SNPs differ on input and output files
written 10.8 years ago by stolarek.ir

Hi, I am using plink v 1.9 to convert my ped file to vcf with command: ./plink --ped file.ped --map file.map --recode vcf --out ped_to_vcf …
Recode phenotype in PLINK
written 10.9 years ago by nazatuls.hassan •

Hi I have converted files gen/sample (using gtool) to ped/map to be used in PLINK with phenotype coded as (0=unaffected 1=affected). However, when I converted …
PLINK: Change affection status
written 11.1 years ago by bsmith030465

Hi, I need to change the affection status in my PLINK files (data1.bed, data1.bim, data1.fam) **to '2' for all samples**. To do this, I was …
PLINK: merge .bed files
written 11.1 years ago by bsmith030465

Hi, I had a set of .bed,.bim, .fam files (myfile1.bed, myfile2.bed, ...) that I wanted to merge to get one file in .bed , bim, …
nan in .bim file generated by plink
written 11.8 years ago by dharl •

Hi all.. I used plink to generate .bed, .bim and .fam files from .ped and .map files. This conversion worked well. When I access the …
Convert Bam To Bed/Fam/Bim
written 14.6 years ago by Anjali •

<p>Hi,</p> <p>I used Bedtools to convert BAM to BED format for my sequencing data. But together with BED I need the corresponding BIM and FAM …