get_gene_list: get_gene_list

In ovrhuman/MultiEWCE: EWCE for Multiple Gene Lists

Description

This returns a character vector of genes (a gene list). The gene_data should be a data frame that contains a column of gene list names (e.g. the column may be called "Phenotype"), and a column of genes (e.g. "Gene"). For example, lets call the following data frame phenotype_to_genes:

Usage

get_gene_list(
  list_name,
  gene_data,
  list_name_column = "Phenotype",
  gene_column = "Gene"
)

Arguments

list_name	The name of the gene list of interest (string)
gene_data	The data frame of gene list names and associated genes (data.frame)
list_name_column	The name of the column in gene_data that contains gene list names (string)
gene_column	The name of the column in gene_data that contains the genes (string)

Details

Phenotype	Gene
"Abnormal heart"	gene X
"Abnormal heart"	gene Y
"Poor vision"	gene Z
"Poor vision"	gene Y
etc...

In the example above, if we wanted to extract genes related to "Abnormal heart", we would run the following example:

Value

A charcter vector of genes associated with the selected list_name

Examples

phenotype_to_genes <- HPOExplorer::load_phenotype_to_genes("phenotype_to_genes.txt")

height_genes <- get_gene_list(list_name = "Abnormality of body height",
                             gene_data = phenotype_to_genes,
                             list_name_column = "Phenotype",
                             gene_column = "Gene")

ovrhuman/MultiEWCE documentation built on Dec. 22, 2021, 5:21 a.m.