diagonal matrix to square matrix Post: 302351510

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Top Forums Shell Programming and Scripting diagonal matrix to square matrix Post 302351510 by yifangt on Tuesday 8th of September 2009 07:54:08 PM

09-08-2009

Registered User

diagonal matrix to square matrix

Hello, all!

I am struggling with a short script to read a diagonal matrix for later retrieval.
1.000 0.234 0.435 0.123 0.012 0.102 0.325 0.412 0.087 0.098
1.000 0.111 0.412 0.115 0.058 0.091 0.190 0.045 0.058
1.000 0.205 0.542 0.335 0.054 0.117 0.203 0.125
1.000 0.587 0.159 0.357 0.258 0.654 0.341
1.000 0.269 0.369 0.687 0.145 0.125
1.000 0.222 0.451 0.134 0.333
1.000 0.112 0.217 0.095
1.000 0.508 0.701
1.000 0.663
1.000

Actually this matrix is the correlation co-efficiency of the gene expression by microarray, so that half matrix contains the same information of the square matrix.

First, the matrix should be aligned with all the 1.000 at the diagonal, i.e.

1.000 0.234 0.435 0.123 0.012 0.102 0.325 0.412 0.087 0.098
1.000 0.111 0.412 0.115 0.058 0.091 0.190 0.045 0.050
1.000 0.205 0.542 0.335 0.054 0.117 0.203 0.125
1.000 0.587 0.159 0.357 0.258 0.654 0.341
1.000 0.269 0.369 0.687 0.145 0.125
1.000 0.222 0.451 0.134 0.333
1.000 0.112 0.217 0.095
1.000 0.508 0.701
1.000 0.663
1.000

as each gene has 1.000 correlation coefficiency with itself.
Then, I want to get a square matrix to fill the missing half by Matrix[i][j]=Matrix[j][i] e.g. Matrix[2][1]= matrix[1][2] etc. I only posted 10 out of 25,000 genes. The real file is a 25,000x25,000 square matrix.
With the sqaure matrix I can easily access any row or column for the co-efficiencies of each individual gene with the others of the genome.
Thanks a lot!

Yifang

Last edited by yifangt; 09-08-2009 at 10:34 PM..

yifangt

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LEARN ABOUT DEBIAN

oakdecode

oakdecode(1)						      General Commands Manual						      oakdecode(1)

NAME

       oakdecode - Decode an OAKT printer stream into human readable form.

SYNOPSIS

       oakdecode [options] <OAKT-file

DESCRIPTION

       oakdecode decodes an OAKT printer stream into human readable form.

       An OAKT printer stream is the printer langauge used by the HP Color LaserJet 1500 and other printers.

COMMAND LINE OPTIONS

       These are the options that can appear on the command line.

       -d basename
	      Basename of .pbm file for saving decompressed planes.

       -r basename
	      Basename of .jbg file for saving raw planes

       -i     Suppress display of image records.

       -o     Print file offsets.

       -D level
	      Set Debug level [0].

EXAMPLES

       Decode an OAKT file created by foo2oak.

       $ oakdecode < testpage.oak
       0d(80) 1 OTHER
       0c(64) Wed Nov 05 16:30:50 2003        a07d3   100005  32001e
       0a(80) testpage.pdf
       14(16) (no args)
       28(16) Source=Tray1
       29(80) PaperType=0 UNK8=2,0,0,0, blanks(63)
       2a(32) Copies=1        UNK=0
       2b(32) papercode=25    xwid=4648       ywid=9000       UNK=0
       33(64)
	       u0      u1      w       h       resx    resy    nBits
	       x0      x0      2128    4300    600     600     x1
       15(16) (no args)
	    bih0     w	   h	l0     bih5   dlen  plen unk yOff P subP
       3c(64) 00010000 2176  256  256 58030020  1050  1056 000   64 3 0
		       DL = 0, D = 0, P = 1, - = 0, XY = 2176 x 256
		       L0 = 256, MX = 32, MY = 0
		       Order   = 3  ILEAVE SMID
		       Options = 88  LRLTWO TPDON TPBON
		       1 stripes, 0 layers, 1 planes
       3c(64) 00010000 2176  256  256 58030020  3668  3680 000  320 3 0
       3c(64) 00010000 2176  256  256 58030020  1463  1472 000  640 3 0
       3c(64) 00010000 2176  256  256 58030020  1975  1984 000  896 3 0
       3c(64) 00010000 2176  224  224 58030020  2744  2752 000 1152 3 0
       3c(64) 00010000 2176  256  256 58030020   988	992 000 1440 3 0
       3c(64) 00010000 2176  256  256 58030020  2892  2896 000 1696 3 0
       3c(64) 00010000 2176  256  256 58030020  3634  3648 000 1952 3 0
       3c(64) 00010000 2176  256  256 58030020  3236  3248 000 2208 3 0
       3c(64) 00010000 2176  256  256 58030020  2279  2288 000 2464 3 0
       3c(64) 00010000 2176  256  256 58030020  3746  3760 000 2720 3 0
       3c(64) 00010000 2176  200  200 58030020  2404  2416 000 2976 3 0
       3c(64) 00010000 2176  256  256 58030020  3114  3120 000 3240 3 0
       3c(64) 00010000 2176   96   96 58030020  1142  1152 000 3496 3 0
       3c(64) 00010000 2176  256  256 58030020  2094  2112 000 3752 3 0
       3c(64) 00010000 2176  256  256 58030020  1319  1328 000 4008 3 0
       3c(64) 00010000 2176   36   36 58030020   208	224 000 4264 3 0
       17(16) (no args)
       18(16) UNK=0
       0b(16) (no args)

FILES

       /usr/bin/oakdecode

SEE ALSO

       foo2oak-wrapper(1), foo2oak(1), jbg2pbm(1)

AUTHOR

       Rick Richardson <rick.richardson@comcast.net>
       http://foo2oak.rkkda.com/