run_coex_partner_workflow: Extract partners of a set of gene-ids, generate summary...

In russHyde/coxpresdbr: Parses and Summarises Data from coxpresdb.jp

Description

Extract partners of a set of gene-ids, generate summary statistics over those neighbours and then cluster the initial gene-ids

Usage

run_coex_partner_workflow(gene_ids, gene_statistics, importer,
  gene_universe = NULL, n_partners = 100, ...)

Arguments

gene_ids	A set of gene identifiers. Should be a subset of the genes in gene_statistics and (if defined) gene_universe.
gene_statistics	A table containing the two-tailed p-values, direction-of-change and gene-ids for all genes that are to be considered in the analysis (any genes that are not in the gene_universe are disregarded).
importer	A CoxpresDbAccessor object.
gene_universe	A set of gene identifiers or NULL. If defined, each of the gene-identifiers should have data present in a row of gene_statistics. If undefined, the universe is taken to be the intersection of all genes in gene_statistics and all genes accessible through the CoxpresDB dataset in importer. Once defined, all genes in gene_ids should be present in gene_universe.
n_partners	The maximum number of partners to pull out for a given source gene from the CoxpresDb database.
...	Other arguments passed to get_coex_partners.

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