genesbyfunctionalinteraction: Find genes of P. falciparum (strain HB3) identified by...
In duncantl/REuPathDB: Interface to REST API of (EuPathDB)

Description Arguments Value

Find Plasmodium falciparum genes identified by the <a href="http://www.cbil.upenn.edu/plasmoMAP">plasmoMAP</a> project to have a functional interaction with the given gene.

Input a gene ID and a minimum interaction likelihood score. Scores range from 2 to 9435, and increasing scores indicate higher confidence. Generally, a likelihood score of 10 or more indicates a high-confidence interaction.

There are 388,969 total predicted protein pairs in the result set, with likelihood scores ranging from 2 to 9435. Below a score of 2, the number of false positives exceed the number of true positives. Most protein-protein interaction pairs (~79%) have a likelihood score of below 10, while about 20% of the pairs have a likelihood score between 10 and 9435 (only 251 pairs, or about 0.06% of the total, have a likelihood score above 100).

Empirical observations of the results show that while many pairs with very low likelihood scores (say between 2-4) are biologically valid, the predicted interactions are likely to be highly accurate as the scores approach a value of 10. In the published manuscript, a score of 14 was used to isolate a high-confidence subset of interactions, where the number of true positives was about 10 times greater than the number of false positives.

`ds_gene_ids`	input a comma delimited set of gene ids, or upload a file
`signature`	Used to pass the Users Signature to the component sites
`min_interaction`	Set a minimum for the likelihood of interaction
`include_only_queries`	Click yes to to restrict the results returned to only those genes which have been input as query ids. This allows you to determine the relatedness of your query set
`min_num_query_matches`	Enter the minimum number of queries you want to match to your genes. If you input 5 genes ids for your query and enter 5 minimum number of queries then the only genes returned would be ones that all 5 queries match
`o-fields`	Single valued attributes of the feature. Provide one or more values. Use comma as a delimter.
`o-tables`	Multi-valued attributes of the feature. Provide one or more values. Use comma as a delimter.
`.convert`	a logical value or a function that controls how the result of the method is returned. If this is a function, the character string or raw vector is passed to this function and it converts it appropriately. If this is a logical value and `TRUE`, then we attempt to convert the result based on its Content-Type returned by the Web server. If this is `FALSE`, the value from the Web server is returned as is.
`.url`	the URL for the Web request. This defaults to the correct value, but can be specified by the caller if the method is available at a different URL, e.g. locally or in a mirror server.
`.json`	a logical value controlling whether to use the JSON or the XML version of the method