View source: R/load_phenotype_to_genes.R
load_phenotype_to_genes | R Documentation |
This is a function for loading the HPO phenotype to genes text file from HPO. It adds the column names and returns as a dataframe. It contains phenotypes annotated with associated genes.
load_phenotype_to_genes(
file = c("phenotype_to_genes.txt", "genes_to_phenotype.txt", "phenotype.hpoa"),
save_dir = file.path(KGExplorer::cache_dir(package = "HPOExplorer"), "data"),
repo = paste("obophenotype", "human-phenotype-ontology", sep = "/"),
tag = "latest",
overwrite = FALSE,
save_tmp = TRUE,
verbose = TRUE
)
file |
name or vector of names of files to be downloaded. If |
save_dir |
Folder where the phenotype to genes text file is/will be stored. |
repo |
Repository name in format "owner/repo". Defaults to |
tag |
tag for the GitHub release to which this data should be attached. |
overwrite |
Should any local files of the same name be overwritten?
default |
save_tmp |
Keep the intermediate annotation text file (before it gets converted to .rds format). |
verbose |
Print messages. |
A data.table of the HPO annotations.
phenotype_to_genes <- load_phenotype_to_genes()
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