get_valid_gene_lists: get valid gene lists

In neurogenomics/MultiEWCE: Multi-Scale Target Explorer

get valid 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,
  list_name_column,
  gene_data,
  annotLevel = 1,
  min_genes = 4,
  verbose = TRUE
)

Arguments

ctd	CellTypeDataset generated using generate_celltype_data.
list_names	character vector of gene list names.
list_name_column	The name of the gene_data column that has the gene list names.
gene_data	data frame of gene list names and genes (see get_gene_lists).
annotLevel	An integer indicating which level of sct_data to analyse (Default: 1).
min_genes	Minimum number of genes per list (default: 4)
verbose	Print messages.

Details

This function gets gene lists that have at least 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

neurogenomics/MultiEWCE documentation built on Sept. 28, 2024, 2:27 a.m.