Read MAP and PED files in PLINK
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3.1 years ago
ft821525 • 0

I want to conduct GWAS analysis using PLINK 1.9. I have created the text files that contain MAP and PED data. However, I could not read the files into PLINK and keep getting errors (attached) I suspect that the problem is the file format, but I have no idea on how can I create MAP/PED files from text file. I searched everywhere for solution but without success. I appreciate if you can help me sort this problem by describing the steps from data.frame in excel to reading the data into PLINK. Thank you!


PLINK erro

PLINK erro


ped file

ped file


My directory

My directory


GWAS PLINK • 3.7k views
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I am confused, what do you mean "from text file"?

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It means that I copied the map and ped data from excel and pasted in text file and saved them with extention of map and ped. The attached is screen shot of the ped data in excel sheet.

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3.1 years ago
Wietje ▴ 220

Could you tell us what error message you got exactly and what your code was? That would help with debugging...

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Microsoft Windows [Version 6.1.7601] Copyright (c) 2009 Microsoft Corporation. All rights reserved.

c:>cd GWAS\plink

c:\GWAS\plink>plink --file hc PLINK v1.90b5.4 64-bit (10 Apr 2018) www.cog-genomics.org/plink/1.9/ (C) 2005-2018 Shaun Purcell, Christopher Chang GNU General Public License v3 Logging to plink.log. Options in effect: --file hc

8108 MB RAM detected; reserving 4054 MB for main workspace. Error: Failed to open hc.map.

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Could you provide an excerpt from the map file? And most importantly - in your directory screenshot the PED and MAP file are listed as text documents, so apparently something went wrong when saving the file. Did you export directly from Excel? I often exported to Notepad (text editor) first with copy-paste and then saved as "all file types" --> then the ".map" and ".ped" ending actually work.

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Many thanks Wietje, the problem was solved by saving the file as you suggested.

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Hi, i followed your method and it becomes a rtf file for some reason...Could you explain it in more detail? Thanks!

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