The mcxarray manual

27 Feb 2006 mcxarray 1.006, 06-058

1. |  | NAME
2. |  | SYNOPSIS
3. |  | DESCRIPTION
4. |  | OPTIONS
5. |  | AUTHOR
6. |  | SEE ALSO

## 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.