Question: How to combine txt file to convert in Plink format
0
gravatar for bha
13 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 • 705 views
ADD COMMENTlink modified 13 months ago by Kevin Blighe33k • written 13 months ago by bha60

please post expected output.

ADD REPLYlink modified 13 months ago • written 13 months ago by cpad011210k

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 13 months ago • written 13 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 13 months ago by Kevin Blighe33k

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 13 months ago by Pierre Lindenbaum115k
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