get_coex_partners: Returns the coexpression partners of a given set of genes
In russHyde/coxpresdbr: Parses and Summarises Data from coxpresdb.jp

Several filters are applied while identifying the coexpression partners of a given set of genes. Only those gene-pairs with a mutual rank below- the user-selected threshold, and for a given input gene _at most_ n_partners are returned.

1 2	get_coex_partners(gene_ids, importer, gene_universe = NULL, n_partners = 100, mr_threshold = NULL)

`gene_ids`	A vector of gene identifiers. All of these should be annotated within the 'coxpresDb' dataset.
`importer`	A `CoxpresDbAccessor`. This allows access to a 'coxpresDb' archive.
`gene_universe`	The genes in the dataframe should be filtered to ensure they are all present in this set. Note that both the entries in `source_id` and `target_id` are filtered to be in this set.
`n_partners`	The maximum number of partners to return for the source gene(s) in `coex_df`. Gene partners will be sorted in order of mutual-rank before selecting the top partners.
`mr_threshold`	All gene-pairs in the returned dataset will have a mutual-rank of at most this value.

If the user provides a gene_universe, the dataframe will only contain genes that are present in this set (the default universe is the entirety of the genes present in the coxpresDB archive).

If the thresholds, number-of-partners or gene_universe are set to NULL, the corresponding filters are not applied to the dataset.

russHyde/coxpresdbr documentation built on Dec. 24, 2019, 11:59 a.m.