gene_summary: wrapper function to find all info about a list of genes

In KatrionaGoldmann/omicAnnotations: Use databases to annotate genomic and transcriptomic data

wrapper function to find all info about a list of genes

Description

wrapper function to find all info about a list of genes

Usage

gene_summary(
  genes,
  verbose = TRUE,
  get_gene_types = TRUE,
  get_gene_description = TRUE,
  get_associated_diseases = TRUE,
  get_publications = FALSE,
  gene_types_df = NULL,
  ncbi_retmax = 50,
  disease_cutoff = 0,
  disease_source = "curated",
  disease_api_token = NULL,
  diseases = c("C20", "C05", "C10", "C17"),
  publication_keywords = c("Rheumatoid", "Autoimmune"),
  publication_split = "OR"
)

Arguments

genes	List of gene names
verbose	Whether to split out the progress
get_gene_types	Highlight interesting genes?
get_gene_description	Whether to find a summary of the gene info
get_associated_diseases	Whether to find the associated diseases
get_publications	Do you want publication info? (This is time consuming if you have a lot of genes)
gene_types_df	A data frame of annotation types with columns for: the annotation name, the contains a character vector for grep command and general info about the gene. If NULL system.file("extdata","immune_genes.txt", package = "omicAnnotations")
ncbi_retmax	The number of NCBI hits to try. If you are struggling to find info try increasing this, although it will become slower (default=50).
disease_cutoff	The DisGeNET Score cutoff
disease_source	The source of the GDA (see https://www.disgenet.org/dbinfo)
disease_api_token	The authentication token by DisGenNet (Sign up here: https://www.disgenet.org/signup/). Then run get_api_key(email, password).
diseases	The MeSH disease classes to use ("C20"=Immune System Diseases)
publication_keywords	Words to search for publications with the genes
publication_split	Whether to use AND or OR when searching the publication keywords (default is OR)

KatrionaGoldmann/omicAnnotations documentation built on June 23, 2022, 2:15 p.m.