get_valid_gene_lists: get valid gene lists

In ovrhuman/MultiEWCE: EWCE for Multiple Gene Lists

Description

Gene lists for EWCE must have 4 or more genes. These genes must also be present in the CTD file (see EWCE docs), and must be unique (occasionally a gene list may contain the same gene repeated. This would cause an error).

Usage

get_valid_gene_lists(
  ctd,
  list_names,
  gene_data,
  list_name_column = "Phenotype",
  gene_column = "Gene"
)

Arguments

ctd	CTD (cell type data file) see EWCE docs
list_names	Vector of gene list names (character vector)
gene_data	data frame containing a gene column and a column of list_names
list_name_column	The name of the column that contains gene list_names (string)
gene_column	The name of the gene column (e.g. "Gene") (string)

Details

This function gets gene lists that have atleast four unique genes that are also present in the CTD file.

Value

A character vector of list_names that are associated with a valid number of genes

Examples

## Not run: 
remove_invalid_gene_lists(ctd,
                          list_names,
                          gene_data,
                          list_names_column = "Phenotype",
                          gene_column = "Gene")

## End(Not run)

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