27 Feb 2006    mcxarray 1.006, 06-058

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NAME

mcxarray - Transform array data to MCL matrices

SYNOPSIS

mcxarray [options] <array data matrix>

mcxarray [-o fname (output file fname)] [-co num (cutoff for output values)] [-gq num (ignore input smaller than)] [-lq num (ignore input larger than)] [-t (work with the transpose)] [-ctr num (add center (for graph-type input))] [--ctr (add center with default value (for graph-type input))] [--01 (remap output to [0,1] interval)] [--cosine (use cosine)] [--pearson (use Pearson correlation (default))] [-tear num (inflate input columns)] [-teartp num (inflate tranposed columns)] [-pi num (inflate the result)] <fname> (array data matrix)

DESCRIPTION

mcxarray reads a data file satisfying the mcl input format (refer to mcxio). By default it will work with the columns as the data vectors (note that mcl matrices are presented as a listing of columns). This can be changed using the -t option.

OPTIONS

-o fname (output file fname)
  
Indeed.
  
-co num (cutoff for output values)
  
Output values smaller than num are removed (set to zero).
  
-gq num (ignore input smaller than)
  
Input values smaller than num are ignored.
  
-lq num (ignore input larger than)
  
Input values larger than num are ignored.
  
-t (work with the transpose)
  
Work with the transpose of the input data matrix.
  
-ctr num (add center (for graph-type input))
  
Add diagonal values to the output according to a (so called) center formula.
  
--ctr (add center with default value (for graph-type input))
  
Same as -ctr 1.0.
  
--01 (remap output to [0,1] interval)
  
Rescale output values so that they are within the [0,1] interval.
  
--cosine (use cosine)
  
Use the cosine as correlation measure.
  
--pearson (use Pearson correlation (default))
  
Compute the Pearson correleation coefficient as the similarity between the data columns.
  
-tear num (inflate input columns)
  
Apply (column-wise) inflation with parameter num to the input values before further processing.
  
-teartp num (inflate tranposed columns)
  
Apply (column-wise) inflation with parameter num to the input values in the transposed matrix before further processing.
  
-pi num (inflate the result)
  
Apply inflation with parameter num to the output values.

AUTHOR

Stijn van Dongen.

SEE ALSO

mcl, mclfaq, and mclfamily for an overview of all the documentation and the utilities in the mcl family.