Files changed (3)
* On the sending end, all outgoing messages must first begin with a message header that specifies the
* On the receiving end, CSeekNetwork also supports the receiving of a \c char array (or a \c string) or a \c float array.
* SeekMiner -x <dset_platform_map> -i <gene_map> -q <query> -P <platform_dir> -p <prep_dir> -n <num_db>
* Users can select between Pearson correlations (\c -z \c pearson) or z-scores of Pearson (\c -z \c z_score).
* Z-scores is the recommended choice because it normalizes the correlation distribution to a standard normal
- * \li \c --norm_subavg. Subtracts each gene's average z-score to reduce the influence of hubby genes.
+ * \li \c --score_cutoff. Cuts off z-scores at a specified value. Z-scores that fall below the cut-off are assigned zero.
+ * \li \c --norm_subavg. Subtracts each gene's average z-score to prevent highly connected genes from influencing the z-score of a gene pair
* \li \c --norm_subavg_plat. Normalizes z-score by subtracting the average across the platform and dividing by its standard deviation.
* Users may also define the datasets that they wish to use for integrations in a query-specific way, using \c -D argument.
- * If this argument is absent, all datasets in the compendium will be integrated. If \c -D is used, the search datasets
+ * Directory that contains the SINFO files, which list a dataset's average z-score between all pairs of genes
+ * and the standard deviation. If this directory is provided, there should be one SINFO file for <b>
+ * When it is running, SeekServer services requests over the network from multiple connected clients
+ * A list of genes that are found by the algorithm to be coexpressed with the query genes and a list of datasets
+ * SeekServer -t <port> -x <dset_platform_map> -i <gene_map> -d <db_dir> -p <prep_dir> -P <platform_dir>
+ * This starts an instance of SeekServer on the indicated port and begins accepting client requests.
+ * When a client request comes in, SeekServer looks for the following sequence of 4 strings that are sent by the client:
+ * \li \c strSearchDataset. Dataset names, as referred by the \c dset_platform_map, to be used for the search.
+ * \li \c strOutputDir. Output directory where intermediate results are generated. Must be a directory that the running user of
+ * \li \c strSearchParameter. A string of the form "1_2_3_4" where each number denotes the following:
+ * 3 - minimum fraction of query required to score each dataset (0 - 1.0). Recommended 0 (no minimum). <br>
+ * Once SeekServer correctly receives the above 4 strings, a search instance using the provided search parameters will
+ * Each outgoing message is generated upon finishing searching the client's query. In general, if the search is successful,
+ * the client expects two arrays from the SeekServer in sequence: a binary float array of dataset weights, and a binary float array
+ * of gene scores. An element at index \a i in the dataset array represents the weight of the dataset with ID = \a i.
+ * These include the following: \c dset_platform_map, \c gene_map, \c db_dir, \c prep_dir, \c platform_dir, \c quant,
- * <td>Tab-delimited text file containing two columns, numerical gene IDs (one-based) and unique gene