Returns a processed CTD table from the ctdR cache populated by
import_CTD, without reaching into the .rda cache files
by hand. Use this instead of load(file.path(cache_dir, "...rda")) when
you need the chemical metadata or the raw interaction table in your own code.
For the chemical gene sets (the input to enrichment engines) use
as_genesets_CTD instead.
Usage
ctd_cache(what = c("chemicals", "interactions"), cache_dir = .ctd_cache_dir())Arguments
- what
Which cached table to return:
"chemicals"a data frame with one row per chemical (
ChemicalID,ChemicalName)."interactions"the long-format interaction table (
ChemicalID,EntrezID,InteractionActions).
- cache_dir
Directory holding the cached CTD files. Defaults to the ctdR user cache populated by
import_CTD.
See also
import_CTD to populate the cache;
as_genesets_CTD for the chemical gene sets.
Examples
# Examples write to a temporary cache, so running them cannot
# disturb CTD data you have already imported. Set the same option
# yourself to keep an analysis isolated from your main cache.
options(ctdR.cache = tempfile())
sample_file <- system.file(
"extdata", "CTD_chem_gene_ixns_sample.csv",
package = "ctdR"
)
import_CTD(sample_file)
#> Reading CTD chemical-gene interactions from: /home/runner/work/_temp/Library/ctdR/extdata/CTD_chem_gene_ixns_sample.csv
#> Filtered to 86 human interactions
#> Mapping genes for 10 chemicals...
#> Warning: 10 ChemicalID(s) appear with more than one ChemicalName in the CTD file; only the first name per ID is retained. Affected IDs: D000082, D001564, D002104, D003907, D004958 ... (and 5 more)
#> CTD data cached successfully in: /tmp/Rtmpt9pODL/file1b1372704522
#> 10 chemicals | 17 unique genes | 0 s
#> CTD release: Mon Jan 01 00:00:00 EST 2024
chem <- ctd_cache("chemicals")
head(chem)
#> # A tibble: 6 × 2
#> ChemicalID ChemicalName
#> <chr> <chr>
#> 1 D000082 Acetaminophen
#> 2 D001564 Benzo(a)pyrene
#> 3 D002104 Cadmium
#> 4 D003907 Dexamethasone
#> 5 D004958 Estradiol
#> 6 D001151 Arsenic