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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
Old 09-08-2009
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..
 

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ZHPTRF(l)								 )								 ZHPTRF(l)

NAME
ZHPTRF - compute the factorization of a complex Hermitian packed matrix A using the Bunch-Kaufman diagonal pivoting method SYNOPSIS
SUBROUTINE ZHPTRF( UPLO, N, AP, IPIV, INFO ) CHARACTER UPLO INTEGER INFO, N INTEGER IPIV( * ) COMPLEX*16 AP( * ) PURPOSE
ZHPTRF computes the factorization of a complex Hermitian packed matrix A using the Bunch-Kaufman diagonal pivoting method: A = U*D*U**H or A = L*D*L**H where U (or L) is a product of permutation and unit upper (lower) triangular matrices, and D is Hermitian and block diagonal with 1-by-1 and 2-by-2 diagonal blocks. ARGUMENTS
UPLO (input) CHARACTER*1 = 'U': Upper triangle of A is stored; = 'L': Lower triangle of A is stored. N (input) INTEGER The order of the matrix A. N >= 0. AP (input/output) COMPLEX*16 array, dimension (N*(N+1)/2) On entry, the upper or lower triangle of the Hermitian matrix A, packed columnwise in a linear array. The j-th column of A is stored in the array AP as follows: if UPLO = 'U', AP(i + (j-1)*j/2) = A(i,j) for 1<=i<=j; if UPLO = 'L', AP(i + (j-1)*(2n-j)/2) = A(i,j) for j<=i<=n. On exit, the block diagonal matrix D and the multipliers used to obtain the factor U or L, stored as a packed triangular matrix overwriting A (see below for further details). IPIV (output) INTEGER array, dimension (N) Details of the interchanges and the block structure of D. If IPIV(k) > 0, then rows and columns k and IPIV(k) were interchanged and D(k,k) is a 1-by-1 diagonal block. If UPLO = 'U' and IPIV(k) = IPIV(k-1) < 0, then rows and columns k-1 and -IPIV(k) were interchanged and D(k-1:k,k-1:k) is a 2-by-2 diagonal block. If UPLO = 'L' and IPIV(k) = IPIV(k+1) < 0, then rows and columns k+1 and -IPIV(k) were interchanged and D(k:k+1,k:k+1) is a 2-by-2 diagonal block. INFO (output) INTEGER = 0: successful exit < 0: if INFO = -i, the i-th argument had an illegal value > 0: if INFO = i, D(i,i) is exactly zero. The factorization has been completed, but the block diagonal matrix D is exactly singu- lar, and division by zero will occur if it is used to solve a system of equations. FURTHER DETAILS
5-96 - Based on modifications by J. Lewis, Boeing Computer Services Company If UPLO = 'U', then A = U*D*U', where U = P(n)*U(n)* ... *P(k)U(k)* ..., i.e., U is a product of terms P(k)*U(k), where k decreases from n to 1 in steps of 1 or 2, and D is a block diagonal matrix with 1-by-1 and 2-by-2 diagonal blocks D(k). P(k) is a permutation matrix as defined by IPIV(k), and U(k) is a unit upper triangular matrix, such that if the diagonal block D(k) is of order s (s = 1 or 2), then ( I v 0 ) k-s U(k) = ( 0 I 0 ) s ( 0 0 I ) n-k k-s s n-k If s = 1, D(k) overwrites A(k,k), and v overwrites A(1:k-1,k). If s = 2, the upper triangle of D(k) overwrites A(k-1,k-1), A(k-1,k), and A(k,k), and v overwrites A(1:k-2,k-1:k). If UPLO = 'L', then A = L*D*L', where L = P(1)*L(1)* ... *P(k)*L(k)* ..., i.e., L is a product of terms P(k)*L(k), where k increases from 1 to n in steps of 1 or 2, and D is a block diagonal matrix with 1-by-1 and 2-by-2 diagonal blocks D(k). P(k) is a permutation matrix as defined by IPIV(k), and L(k) is a unit lower triangular matrix, such that if the diagonal block D(k) is of order s (s = 1 or 2), then ( I 0 0 ) k-1 L(k) = ( 0 I 0 ) s ( 0 v I ) n-k-s+1 k-1 s n-k-s+1 If s = 1, D(k) overwrites A(k,k), and v overwrites A(k+1:n,k). If s = 2, the lower triangle of D(k) overwrites A(k,k), A(k+1,k), and A(k+1,k+1), and v overwrites A(k+2:n,k:k+1). LAPACK version 3.0 15 June 2000 ZHPTRF(l)
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