Transpose Matrix

Transpose the rows and columns of tab-delimited matrix data.

$$\begin{pmatrix} a_{1,1} & \cdots & a_{1,n}\\ \vdots & \ddots & \vdots \\ \vdots & \ddots & \vdots \\ a_{m,1} & \cdots & a_{m,n} \\ \end{pmatrix} \rightarrow \begin{pmatrix} a_{1,1} & \cdots & \cdots & a_{1,m}\\ \vdots & \ddots & \ddots & \vdots \\ a_{n,1} & \cdots & \cdots & a_{n,m} \\ \end{pmatrix}$$

File input (CDT/TAB)

This script does not restrict selection of file inputs because a variety of file extensions may be parsed out for the tab-delimited (numeric) matrix. The tool supports bulk selection and processing of files.

Select Starting Row/Column

These integers indicate the last header columns or row labels. By default they are set to follow CDT format specifications but can be adjusted if you have some other tab-delimited file format with different header starts.

Output

Each matrix file is transposed and written with the _TRANSPOSE suffix appended and an extension that matches the input file's extension. For example, SomeMatrixFile.cdt would be scaled and written to SomeMatrixFile_TRANSPOSE.cdt.

Output GZip

Toggling this allows the user to write output to a compressed file format using a general compression (gzip) which has the added advantage of speeding up the execution time by shrinking the I/O load (esp for large output). The .gz extension will be appended as appropriate.

Command Line Interface

Usage:

java -jar ScriptManager.jar read-analysis transpose-matrix [-hV] [-z] [-l=<startCOL>]
[-o=<output>] [-r=<startROW>] <matrix>

Positional Input

This tool takes a matrix file in TAB/CDT format for input.

Output Options

Option	Description
-o, --output=<output>	specify output filename
-z, --gzip	gzip output (default=false)

Coord Start Options

Option	Description
-r, --start-row	row to start transposing the matrix (zero indexed)
-l, --start-col	column to start transposing the matrix (zero indexed)