Skip to contents

Build Adjacency Matrices for Physical Interactions from STRING (POST API)

Source: R/stringdb_adjacency.R
stringdb_adjacency.Rd

Constructs weighted and binary adj matrices for physical protein-protein interactions using a POST request to the STRING database API.

Usage

stringdb_adjacency(
  genes,
  species = 9606,
  required_score = 400,
  keep_all_genes = TRUE,
  verbose = TRUE
)

Arguments

genes

A character vector of gene symbols or identifiers, e.g., c("TP53", "BRCA1", ...).

species

Integer. NCBI taxonomy ID of the species. Default is 9606 (human).

required_score

Integer in \[0,1000\]. Minimum confidence score for interactions. Default is 400.

keep_all_genes

Logical. If TRUE (default), includes all input genes in the final matrix even if unmapped.

verbose

Logical. If TRUE, displays progress messages. Default is TRUE.

Value

A list containing:

  • weighted: A square numeric adjacency matrix with scores as weights.

  • binary: A corresponding binary (0/1) adjacency matrix.

Details

This function:

  1. Maps input genes to STRING internal IDs.

  2. Uses a POST request to retrieve physical protein-protein interactions from STRING.

  3. Builds a weighted adjacency matrix using the STRING combined score.

  4. Builds a binary adjacency matrix indicating presence/absence.

Genes not mapped to STRING are optionally retained as zero rows/columns if keep_all_genes = TRUE.

Note

Requires packages: STRINGdb, httr, jsonlite.

Examples

data(toy_counts)
genes <- selgene(
    object = toy_counts[[1]],
    top_n = 5,
    cell_type = "T_cells",
    cell_type_col = "CELL_TYPE",
    remove_rib = TRUE,
    remove_mt = TRUE,
    assay = "counts"
)
#> Using SCE assay 'counts' (log-normalized).
#> Subsetted to 40 cells where CELL_TYPE = 'T_cells'.
#> Removed mitochondrial genes matching '^MT-'.
#> Removed ribosomal genes matching '^RP[SL]'.
#> Top 5 genes selected based on mean expression.

str_res <- stringdb_adjacency(
    genes = genes,
    species = 9606,
    required_score = 900,
    keep_all_genes = FALSE
)
#> Initializing STRINGdb...
#> Registered S3 method overwritten by 'gplots':
#>   method         from     
#>   reorder.factor DescTools
#> Mapping genes to STRING IDs...
#> Mapped 5 genes to STRING IDs.
#> Retrieving **physical** interactions from STRING API...
#> Found 3 STRING physical interactions.
#> Adjacency matrices constructed successfully.
wadj_truth <- str_res$weighted
toy_adj_matrix <- str_res$binary