get_string_ppi_matrix: Protein-protein interaction (PPIs) from STRING.
In alorchhota/spice: SPICE: Spanning tree based inference of co-expression networks

Description Usage Arguments Details Value Examples

This function generates a matrix of PPI scores available in STRING database within a given set of genes.

get_string_ppi_matrix(
  genes,
  directed = FALSE,
  version = "11",
  species = 9606,
  score.threshold = 0,
  string.dir = "",
  max.homology.bitscore = Inf,
  benchmark.pathway = NULL,
  normalize.score = T
)

`genes`	character vector. gene names (HGNC gene symbols).
`directed`	logical. Directed interactions?
`version`	character. Version of STRING database.
`species`	numeric. Species code for STRING (9606 for homo sapiens).
`score.threshold`	numeric. A value between 0 and 1000. Any score below `score.threshold` will be replaced by 0.
`string.dir`	character. Local directory where STRING database will be stored locally so that it can be used offline. If `string.dir = ""`, a temporary directory is used.
`max.homology.bitscore`	numeric. Maximum homology score. Use `0` to filter all interactions between homologous proteins, and `Inf` not to filter any interaction.
`benchmark.pathway`	character. Pathway type to benchmark. Examples: `"KEGG", "REACTOME", "BIOCARTA", "Disease", "Pfam", "NCI", "ECOCYC"`. Use `NULL` to avoid benchmarking. If a pathway type is given, an interaction will have a non-zero score only if both genes are present in at least one pathway.
`normalize.score`	logical. Should the scores be normalized? If `TRUE`, the scores will be divided by 1000. Consequently, each score will be between 0 and 1.

Note: all the genes are expected as HGNC gene symbols.

A 2-dimensional matrix with interactions between the given genes. Note: any gene that cannot be mapped to a protein in STRING will be excluded.

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genes = c("TP53", "RBM3", "SF3", "LIM12", "MDM4", "TMEM160",
          "TP53BP2", "MDM2", "PDR", "MEG3", "EGFR")
interactions = get_string_ppi_matrix(genes, version = "11")