SVDMAN.CC
Source:
Target:
Type:
Version: 0.1
Date: 8/15/2000
Los Alamos in-house version
Version: 0.9b
Date: 2/9/2001
Make the subroutines more robust and introduce XML style documentation for
the source code.
Packages:
Includes:
Blocks:
main()
Kind:
Authors:
Michael Wall, Los Alamos National Laboratory/mewall@lanl.gov
Patricia Dyck, Los Alamos National Laboratory/tdyck@lanl.gov
Comments:
This program takes as input a file containing a matrix of gene
expression values for multiple experiments obtained from, e.g.,
microarrays. It performs singular value decomposition (SVD) upon
the matrix and can write the SVD as separate files U, VT, S and
B=S.VT. A threshold is applied to columns of U in order to
identify gene groupings for each column, or mode, and the
groupings are output as the row label along with the relative
sign +/- indicating the direction of response of the gene within
the group.
The analysis can be evaluated by systematically removing a column
from the data array, calculating the SVD, and interpolating B to
estimate the values for the missing assay. A version of the
missing column in the original data matrix is calculated using
these interpolated values, then the calculated column is compared
with the column of missing data using a Pearson correlation.
this matrix with the original values as a metric of the success
of the program. Each of the columns but the first and last is
evaluated in this way, and the results are output in a file.
Usage:
Execution:
svdman -i [ifname] { -options {[args]} }
Commands:
Required:
Options:
-o
[string
ofbase]
ofbase:
output filename base
-thresh
[double
threshold]
threshold:
A scale for the threshold value beneath which an ORF does not belong to an eigenvector
-writesvd:
flag to write SVD components U, S, VT and B to files.
-minus:
flag to invert the sign of the matrix elements for U, VT and B
-submean:
flag to subtract the row mean value from each row
-evaluate:
flag to check for self-consistency using an interpolation procedure
Inputs:
Source:
file
Format:
Comments:
Tab-delimited ASCII file. Labels at the top and left. First element is blank.
Outputs:
Destination:
file
Name:
Format:
Comments:
Destination:
file
Name:
Format:
Comments:
SVD matrix U (Columns are left singular vectors)
Destination:
file
Name:
Format:
Comments:
SVD matrix VT (Rows are right singular vectors)
Destination:
file
Name:
Format:
Comments:
Destination:
file
Name:
Format:
Comments:
Returns:
Parameters:
int argc; // Number of command-line arguments
char** argv; // Command-line arguments
Build:
Dependencies:
svdtool.o
libclasvd.a
libF77.a
svd.h
Compile:
g++ -O2 -I./F2CLIBS -c svdman.cc
g++ -O2 -I./F2CLIBS -o svdman svdman.o svdtool.o libclasvd.a libF77.a -lm
Platforms:
RedHatLinux version 7.0
Compilers:
RedHatLinux version 6.1
Compilers: