ewce_para: EWCE parallel

In ovrhuman/MultiEWCE: EWCE for Multiple Gene Lists

Description

Runs EWCE in parallel on multiple gene lists.

Usage

ewce_para(
  list_names,
  gene_data,
  list_name_column = "Phenotype",
  gene_column = "Gene",
  results_directory,
  ctd_file,
  background_genes,
  bootstrap_reps,
  annotation_Level,
  genes_Species,
  ctd_Species,
  cores
)

Arguments

list_names	character vector of gene list names
gene_data	data frame of gene list names and genes (see ?get_gene_list)
list_name_column	The name of the gene_data column that has the gene list names
gene_column	The name of the gene_data column that contains the genes
results_directory	The desired output filepath for results to be saved
ctd_file	The cell type data object for EWCE analysis (see EWCE docs)
background_genes	The background geneset for EWCE analysis (see EWCE docs)
bootstrap_reps	The number of bootstrap reps (int) (e.g. 100000)
annotation_Level	The level of desired cell resolution from the CTD
genes_Species	The species of gene lists (string) "human" or "mouse"
ctd_Species	"human" or "mouse" (string)
cores	The number of cores to run in parallel (e.g. 8) (int)

Value

True if analysis was sucessful. The results will then be saved at "(results_directory)/(list_name).rds"

Examples

## Not run: 
gene_data <- HPOExplorer::load_phenotype_to_genes("phenotype_to_genes.txt")
ctd <- load_example_CTD()
list_names <- unique(gene_data$Phenotype)[1:10]
ewce_para(list_names, gene_data, results_directory ="results",ctd_file = ctd,
          background_genes = unique(gene_data$Gene), bootstrap_reps = 10,
          annotation_Level = 1, genes_Species = "human", ctd_Species = "human",
          cores = 1)


## End(Not run)

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