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Full Discussion: diagonal matrix to square matrix
Top Forums Shell Programming and Scripting diagonal matrix to square matrix Post 302351785 by yifangt on Wednesday 9th of September 2009 01:50:18 PM
Old 09-09-2009
Yes, you are right. The original matrix is NOT a diagonal one. It is upper half symmetric with 1.000 in all the "diagonal" positions.

---------- Post updated at 01:32 PM ---------- Previous update was at 01:30 PM ----------

Thanks, I need to digest your script first. I am just a newbe in shell script and PERL programming.

---------- Post updated at 01:50 PM ---------- Previous update was at 01:32 PM ----------

That's a great solution! Thanks you Tyler!

When I tried to convert my 25000x25000 matrix, I got the "Out of memory!" message and the program stopped. Another problem I noticed is, after I checked the original data, there is ID for each row, i.e.:
"244901_AT" 1.000 0.234 0.435 0.123 0.012 0.102 0.325 0.412 0.087 0.098
"243903_AT" 1.000 0.111 0.412 0.115 0.058 0.091 0.190 0.045 0.058
"244501_AT" 1.000 0.205 0.542 0.335 0.054 0.117 0.203 0.125
"254902_AT" 1.000 0.587 0.159 0.357 0.258 0.654 0.341
"247906_AT" 1.000 0.269 0.369 0.687 0.145 0.125
"242901_AT" 1.000 0.222 0.451 0.134 0.333
"243906_AT" 1.000 0.112 0.217 0.095
"244908_AT" 1.000 0.508 0.701
"294902_AT" 1.000 0.663
"245902_AT" 1.000

and the output square matrix should be like this:
"244901_AT" 1.000 0.234 0.435 0.123 0.012 0.102 0.325 0.412 0.087 0.098
"243903_AT" 0.234 1.000 0.111 0.412 0.115 0.058 0.091 0.190 0.045 0.058
"244501_AT" 0.435 0.111 1.000 0.205 0.542 0.335 0.054 0.117 0.203 0.125
"254902_AT" 0.123 0.412 0.205 1.000 0.587 0.159 0.357 0.258 0.654 0.341
"247906_AT" 0.012 0.115 0.542 0.587 1.000 0.269 0.369 0.687 0.145 0.125
"242901_AT" 0.102 0.058 0.335 0.159 0.269 1.000 0.222 0.451 0.134 0.333
"243906_AT" 0.325 0.091 0.054 0.357 0.369 0.222 1.000 0.112 0.217 0.095
"244908_AT" 0.412 0.190 0.117 0.258 0.687 0.451 0.112 1.000 0.508 0.701
"294902_AT" 0.087 0.045 0.203 0.654 0.145 0.134 0.217 0.508 1.000 0.663
"245902_AT" 0.098 0.058 0.125 0.341 0.125 0.333 0.095 0.701 0.663 1.000

Then I can retrieve each gene by grep the ID of the first column of each row. I should have posted this information first. Sorry about this. Thanks again Tyler!
 

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