Aggregate Data

Compile data from tab-delimited file into matrix according to user-specified metric.

Aggregation Method Options

• Sum
• Average
• Median
• Mode
• Min
• Max
• Positional Variance

Command Line Interface

Usage:

java -jar ScriptManager.jar read-analysis aggregate-data [--sum | --avg | --med |
--mod | --min | --max | --var] [-fhmV] [-l=<startCOL>] [-o=<output>]
[-r=<startROW>] [<inputFiles>...]

The AggregateData tool is used to process a bunch of matrix files into one matrix file.

Input Options

Since this tool process a bunch of files together, there are two ways of feeding input files:

(1) You can list them out in the command line tool,

java -jar ScriptManager.jar read-analysis aggregate-data matFile1 matFile2 ... matFileX <OPTIONS>

(2) or you can write all the paths for all your files in a single file and pass that as the input using the -f flag

java -jar ScriptManager.jar read-analysis aggregate-data inputFile -f <OPTIONS>

where inputFile is listed out line by line:

/path/to/matFile1
/path/to/matFile2
...
/path/to/matFileX

Note that absolute file paths are easier to work with. For relative paths, you'll have to check that they are built with respect to the ScriptManager directory.

Output Options

Option	Description
-m, --merge	merge to one output file
-o, --output=<output>	Specify output file, default is "aggregate_matrix.txt" or the input filename if -f flag used
-z, --gzip	gzip output (default=false)

The file output can be specified by the user using this flag. Otherwise the output will be aggregate_matrix.txt in the same directory as ScriptManager. Or based on the input filename if the -f flag is used.

Aggregation Method Options

Option	Description
--sum	use summation method (default)
--avg	use average method
--med	use median method
--mod	use mode method
--min	use minimum method
--max	use maximum method
--var	use positional variance method

Coord Start Options

Option	Description
-r, --start-row
-l, --start-col