Question: How to combine txt file to convert in Plink format
0
gravatar for bha
2.4 years ago by
bha60
bha60 wrote:

My 26 data files (.txt) (imputed genotypes for each chromosome) look like:

CHR SNP1 SNP2 SNP3
1   3   1   2   3 
1   3   0   2   1
1   0   0   1   0
1   0   3   3   1
1   1   1   0   2

CHR SNP1 SNP2 SNP3
2   1   1   2   2 
2   0   3   1   1
2   0   0   1   0
2   0   3   3   2
2   3   2   0   1

How I can convert them in plink format (.map and .ped)?

snp R • 1.3k views
ADD COMMENTlink modified 2.4 years ago by Kevin Blighe56k • written 2.4 years ago by bha60

please post expected output.

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by cpad011212k

ID SNP1 SNP2 SNP3

17 3 1 2 3

25 3 0 2 1

29 0 0 1 0

99 0 3 3 1

81 1 1 0 2

similarly other 25 files for chromosome 2,3,.....26.

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by bha60

Hi bha, I have edited your post to make it more legible. When you're posting code or output from a command or file, make use of the 'Code Sample' button (the one with 101 010). Highlight the text and then click the button.

ADD REPLYlink written 2.4 years ago by Kevin Blighe56k

Hello bha!

It appears that your post has been cross-posted to another site: https://stackoverflow.com/questions/47225587/

This is typically not recommended as it runs the risk of annoying people in both communities.

ADD REPLYlink written 2.4 years ago by Pierre Lindenbaum127k
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