Utility functions — utils

Functions to support other functions.

cache_dir(package = "KGExplorer")

example_dat(
  types = c("omim_id", "orphanet_id", "decipher_id", "hpo_id", "gene"),
  rm_types = NULL
)

get_data(
  file,
  tag = "latest",
  repo = "neurogenomics/KGExplorer",
  save_dir = cache_dir(),
  add_version = FALSE,
  overwrite = TRUE
)

messager(..., v = Sys.getenv("VERBOSE") != "FALSE", parallel = FALSE)

report_filter(g1, g2, cols, suffix = "remain after filtering.")

report_missing(dat, id_col, report_col)

stopper(..., v = TRUE)

Arguments

package: a character string giving the name of an R package
types: Types of IDs to include in the data.
file: name or vector of names of files to be downloaded. If NULL, all assets attached to the release will be downloaded.
tag: tag for the GitHub release to which this data should be attached.
repo: Repository name in format "owner/repo". Defaults to guess_repo().
save_dir: Directory to save data to.
add_version: Add the release version to the returned object's attributes
overwrite: Should any local files of the same name be overwritten? default TRUE.
v: Whether to print messages or not.
parallel: Whether to enable message print when wrapped in parallelised functions.

Value

Merged data.

Cache directory path.

data.table

Path to downloaded file or the object itself (when ".rds" format).

Null

Functions

cache_dir(): utils_ Cache directory

Provides the path to the package-wide cache directory.
example_dat(): utils_ Example data

Construct an example data.table containing diseases, phenotype, and/or genes.
get_data(): utils_ Get remote data

Download remotely stored data via pb_download.
messager(): utils_ Print messages

Conditionally print messages. Allows developers to easily control verbosity of functions, and meet Bioconductor requirements that dictate the message must first be stored to a variable before passing to message.
report_filter(): utils_
report_missing(): utils_
stopper(): utils_ Stop messages

Conditionally print stop messages. Allows developers to easily control verbosity of functions, and meet Bioconductor requirements that dictate the stop message must first be stored to a variable before passing to stop.

Examples

save_dir <- cache_dir
dat <- example_dat()