CollecTRI is a comprehensive resource of transcriptional regulation, published in 2023, consisting of 14 resources and original literature curation.
Usage
collectri(
resources = NULL,
organism = 9606L,
references_by_resource = TRUE,
exclude = NULL,
strict_evidences = TRUE,
genesymbol_resource = NULL,
...
)
Arguments
- resources
interactions not reported in these databases are removed. See
get_interaction_resources
for more information.- organism
Character or integer: Name or NCBI Taxonomy ID of one or organisms. The web service currently provides interactions for human, mouse and rat. For other organisms, the data will be translated by orthologous gene pairs from human. In this case, only one organism can be provided.
- references_by_resource
if FALSE, removes the resource name prefixes from the references (PubMed IDs); this way the information which reference comes from which resource will be lost and the PubMed IDs will be unique.
- exclude
Character: datasets or resources to exclude.
- strict_evidences
Logical: restrict the evidences to the queried datasets and resources. If set to FALSE, the directions and effect signs and references might be based on other datasets and resources. In case of CollecTRI this is not desirable for most of the applications. For most of the other interaction querying functions it is `FALSE` by default.
- genesymbol_resource
Character: either "uniprot" or "ensembl". The former leaves intact the gene symbols returned by the web service, originally set from UniProt. The latter updates the gene symbols from Ensembl, which uses a slightly different gene symbol standard. In this case a few records will be duplicated, where Ensembl provides ambiguous translation.
- ...
Optional additional arguments, passed to
import_transcriptional_interactions
.
Examples
collectri_grn <- collectri()
#> NULL
collectri_grn
#> # A tibble: 64,495 × 15
#> source target source_genesymbol target_genesymbol is_directed is_stimulation
#> <chr> <chr> <chr> <chr> <int> <int>
#> 1 P01106 O14746 MYC TERT 1 1
#> 2 P17947 P02818 SPI1 BGLAP 1 1
#> 3 COMPLE… P05412 FOSL1_JUNB JUN 1 1
#> 4 COMPLE… P05412 FOS_JUN JUN 1 1
#> 5 COMPLE… P05412 FOS_JUNB JUN 1 1
#> 6 COMPLE… P05412 FOSL2_JUND JUN 1 1
#> 7 COMPLE… P05412 FOSL2_JUN JUN 1 1
#> 8 COMPLE… P05412 JUN JUN 1 1
#> 9 COMPLE… P05412 FOSB_JUNB JUN 1 1
#> 10 COMPLE… P05412 JUNB JUN 1 1
#> # ℹ 64,485 more rows
#> # ℹ 9 more variables: is_inhibition <int>, consensus_direction <int>,
#> # consensus_stimulation <int>, consensus_inhibition <int>, sources <chr>,
#> # references <chr>, curation_effort <int>, n_references <int>,
#> # n_resources <int>