Command-line Interface Input File Descriptions

The data Directory

There are three types of input files that the user needs to create in the data directory. The first two are of identical type to those described for GoMiner - a total genes file and one or more changed-gene files. The difference with GoMiner is that GoMiner accepts only a single changed genes file. The third type of file is a list, one entry per line, of the names of the changed-gene files. Only the base name is entered, not the full pathname. The order of the file names is important if the user wishes the results in the visualizations in the integrative output files to appear in a particular order.

The user has the option of creating additional data directories to help organize the experimental results, and/or using the same data directory for multiple experiments. Note however that the name of the total genes file is used for naming the main output subdirectory, and an output subdirectory within the same data directory will be overwritten if a total genes file with the same name as a previous one is re-used.

The config Directory

The config directory starts out a generic.config file. The file generic.config should be copied to meaningfulName.config and archived as such each time a new set of files or other parameter values are used. The desired parameter values should entered or, in some cases, the default parameters accepted as is.

As with the data directory, the user has the option of creating additional config directories, and/or using the same config directory for multiple experiments. There seems to be little advantage to having multiple config directories, however, as it is quite convenient to have multiple config files within a single config directory.

Web Interface Input

A variant of this format is used for the web interface.

GoMiner™ is a development of the Genomics and Pharmacology Facility, Developmental Therapeutics Branch (DTB), Center for Cancer Research (CCR), National Cancer Institute (NCI).

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