Gets the unfinished gene list names. It reads the file names in the results directory and uses this to deduce which gene lists have already been analysed. This means you can pause the analysis of multiple gene lists and it will not re-analyse the already completed ones when you start again.
get_unfinished_list_names(list_names, save_dir_tmp)character vector of gene list names.
Folder to save intermediate results files to
(one file per gene list). Set to NULL to skip saving temporary files.
A character vector of list_names that still need to be analysed.
gene_data <- HPOExplorer::load_phenotype_to_genes()
#> Reading cached RDS file: phenotype_to_genes.txt
#> + Version: v2023-10-09
list_names <- unique(gene_data$hpo_id)[seq(3)]
save_dir_tmp <- file.path(tempdir(),"results")
ctd <- load_example_ctd()
res_files <- ewce_para(ctd = ctd,
gene_data = gene_data,
list_names = list_names,
reps = 10,
save_dir_tmp = save_dir_tmp)
#> Useing cached bg.
#> + Version: 2023-11-14
#> Computing gene counts.
unfinished <- get_unfinished_list_names(list_names = gene_data$hpo_id,
save_dir_tmp = save_dir_tmp)