svr_find_hypos_for_cluster

Get candidates for a specific role by finding genes with no real assignment of function yet that are connected to a cluster. We will consider a hypothetical "connected to a cluster" iff

    1. it has a strong functional coupling score to a member of the cluster or
    2. it occurs between the bounding members of the cluster

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Example:

    svr_gap_filled_reactions_and_roles -g 273035.4 | svr_find_clusters_relevant_to_role -g 273035.4 -r 2 -n 100 | svr_find_hypos_for_cluster

would produce a 5-column table [Genome,reaction,role,cluster-of-genes-connected-to-role,peg-for-hypothetical]

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The standard input should be a tab-separated table (i.e., each line is a tab-separated set of fields). Normally, the last field in each line would contain a cluster represented as a comma-separated list of genes. If some other column contains the clusters, use

    -c N

where N is the column (from 1) that contains the role in each case.

This is a pipe command. The input is taken from the standard input, and the output is to the standard output.

Command-Line Options

-c N

Specifies which column in the input table contains the clusters. Defaults to the last column in the input file.

Output Format

The standard output is a tab-delimited file. Each line will contain the input fields followed by a score and a PEG with a hypothetical function that is connected to the cluster. The score is either the functional-coupling score or 0 (for a hypo that is embedded, but not functionally coupled).