convert_gene_list_settings_evaluation: Convert gene list to correct settings format for evaluation...

In browaeysrobin/nichenetr: Modeling Intercellular Communication by Linking Ligands to Target Genes with NicheNet

Convert gene list to correct settings format for evaluation of target gene prediction.

Description

convert_gene_list_settings_evaluation Converts a gene list to correct settings format for evaluation of target gene prediction.

Usage

convert_gene_list_settings_evaluation(gene_list, name, ligands_oi, background)

Arguments

gene_list	A character vector of target gene names
name	The name that will be given to the setting
ligands_oi	The possibly active ligands
background	A character vector of names of genes that are not target genes. If genes present in the gene list are in this vector of background gene names, these genes will be removed from the background.

Value

A list with following elements: $name, $from, $response

Examples

## Not run: 
weighted_networks = construct_weighted_networks(lr_network, sig_network, gr_network, source_weights_df)
all_genes = unique(c(weighted_networks$gr$from,weighted_networks$gr$to,weighted_networks$lr_sig$from, weighted_networks$lr_sig$to))
gene_list = c("ID1","ID2","ID3")
setting = list(convert_gene_list_settings_evaluation(gene_list = c("ID1","ID2","ID3"), name = "test",ligands_oi = "TGFB1", background = all_genes))

## End(Not run)

browaeysrobin/nichenetr documentation built on Sept. 9, 2024, 11:25 a.m.