CTD Chemical-Gene Interactions File

CTDFile is a BiocFile subclass representing a Comparative Toxicogenomics Database (CTD) chemical-gene interactions file (CTD_chem_gene_ixns.csv or its gzip-compressed .csv.gz form). Pair it with import to read the file into R following the Bioconductor BiocIO import/export convention, as an alternative to the side-effecting import_CTD caching workflow.

In ctdR, CTD always denotes the Comparative Toxicogenomics Database (https://ctdbase.org). The class is named CTDFile (not CTD) to avoid confusion with unrelated software that shares the acronym (the CRAN package CTD is a graph algorithm; the ctd object in EWCE is a cell-type dataset).

Usage

CTDFile(resource)

# S4 method for class 'CTDFile,ANY,ANY'
import(con, format, text, ...)

Arguments

resource

Character scalar: a local path or a URL to the CTD chemical-gene interactions file.

con

A CTDFile object to import.

format

Ignored; present for compatibility with the BiocIO import generic.

text

Ignored; present for compatibility with the BiocIO import generic.

...

Additional arguments (currently unused).

Value

CTDFile() returns a CTDFile object. import() on a CTDFile returns a DataFrame of validated human (OrganismID 9606) CTD chemical-gene interactions.

Data Licensing Disclaimer

This package does not bundle or redistribute any CTD data. The Comparative Toxicogenomics Database is maintained by NC State University and its data are subject to specific licensing terms. Users are responsible for downloading the data directly from https://ctdbase.org and for complying with the CTD Terms of Service (https://ctdbase.org/about/legal.jsp).

See also

import_CTD for the caching workflow required before enrichment_CTD; BiocFile for the parent class.

Examples

sample_file <- system.file(
    "extdata", "CTD_chem_gene_ixns_sample.csv",
    package = "ctdR"
)
ctd_file <- CTDFile(sample_file)
ctd_file
#> CTDFile object
#> resource: /home/runner/work/_temp/Library/ctdR/extdata/CTD_chem_gene_ixns_sample.csv 
interactions <- BiocIO::import(ctd_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
head(interactions)
#> DataFrame with 6 rows and 11 columns
#>    ChemicalName  ChemicalID       CasRN  GeneSymbol      GeneID   GeneForms
#>     <character> <character> <character> <character> <character> <character>
#> 1 Acetaminophen     D000082    103-90-2         TNF        7124        gene
#> 2 Acetaminophen     D000082    103-90-2         IL6        3569        gene
#> 3 Acetaminophen     D000082    103-90-2        TP53        7157        gene
#> 4 Acetaminophen     D000082    103-90-2       BRCA1         672        gene
#> 5 Acetaminophen     D000082    103-90-2        EGFR        1956        gene
#> 6 Acetaminophen     D000082    103-90-2         MYC        4609        gene
#>       Organism  OrganismID            Interaction   InteractionActions
#>    <character> <character>            <character>          <character>
#> 1 Homo sapiens        9606 Acetaminophen affect.. increases^expression
#> 2 Homo sapiens        9606 Acetaminophen affect.. increases^expression
#> 3 Homo sapiens        9606 Acetaminophen affect.. decreases^expression
#> 4 Homo sapiens        9606 Acetaminophen affect.. decreases^expression
#> 5 Homo sapiens        9606 Acetaminophen affect.. increases^expression
#> 6 Homo sapiens        9606 Acetaminophen affect.. increases^expression
#>     PubMedIDs
#>   <character>
#> 1    12345678
#> 2    12345679
#> 3    12345680
#> 4    12345681
#> 5    12345682
#> 6    12345683