Question: How to combine txt file to convert in Plink format
0
gravatar for bha
7 months 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 • 447 views
ADD COMMENTlink modified 7 months ago by Kevin Blighe21k • written 7 months ago by bha60

please post expected output.

ADD REPLYlink modified 7 months ago • written 7 months ago by cpad01126.3k

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 7 months ago • written 7 months 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 7 months ago by Kevin Blighe21k

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 7 months ago by Pierre Lindenbaum108k
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