Using a molecular neighborhood, target and indication summaries for all genes from Open Targets.
Arguments
- napistu_list
A list containing loaded assets and bindings to Python modules.
- sbml_dfs
SBML_dfs - the core pathway representation of the Napistu Python library
- napistu_graph
Network graph - a Python igraph subclass with Napistu-specific attributes and methods
- species_identifiers
Species identifier mappings
- precomputed_distances
optional, distances between species nodes
- species_names
A tibble containing the names of all genes, proteins, molecules, etc
- identifiers_nest
A tibble with one row per ontology and a nested tibble containing all the identifiers and their corresponding molecular species
- python_modules
A named list of Python modules: `napistu`
- python_environment
- napistu_config
A `napistu_config` object dictating how the `napistu_list` was initialized
- loaded_at
A date-time object indicating when `napistu_list` was initialized
- neighborhood_summary_table
tibble produced by
create_neighborhood_summary_table
Examples
suppressPackageStartupMessages(library(dplyr))
setup_napistu_list(create_napistu_config())
#>
#> ── Setting up Napistu environment ──────────────────────────────────────────────
#> No Python configuration specified, setting up conda environment
#> Using existing conda environment "napistu-config"
#> Python version 3.11 meets requirements
#> No assets configuration specified, loading bundled package data
#> Loading sbml_dfs from sbml_dfs.pkl
#> Error in value[[3L]](cond): Failed to load sbml_dfs from
#> /home/runner/work/_temp/Library/napistu.r/extdata/test_pathway/sbml_dfs.pkl:
#> ImportError: /usr/lib/x86_64-linux-gnu/libcrypto.so.3: version `OPENSSL_3.3.0'
#> not found (required by
#> /usr/share/miniconda/envs/napistu-config/lib/python3.11/lib-dynload/_ssl.cpython-311-x86_64-linux-gnu.so)
#> Run `reticulate::py_last_error()` for details.
species_id <- random_species(napistu_list)
#> Error: object 'napistu_list' not found
neighborhood_summary_table <- create_neighborhood_table(
napistu_list,
species_id,
max_steps = 7L
) %>%
create_neighborhood_summary_table()
#> Error: object 'napistu_list' not found
# TO DO - uncomment once https://github.com/napistu/napistu/issues/14 is addressed
# summarize_diseases(
# napistu_list,
# neighborhood_summary_table
# )