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Draft polarity signs for a panel from public databases

Source: R/polarity_table.R
dmsa_polarity_fetch.Rd

Queries public signed-relationship resources for the genes of a cascade and returns a DRAFT polarity table for a curator to check. It does not decide anything on its own, and it is deliberately unwilling to guess.

Usage

dmsa_polarity_fetch(
  sets,
  anchors = NULL,
  sources = c("go", "omnipath"),
  max_genes = 200L,
  quiet = FALSE
)

Arguments

sets

A dmsa_sets or dmsa_selection whose genes to draft signs for, or a character vector of gene symbols.

anchors

Named list mapping system_id to the anchor genes that define that system's activation tone. Required for anything except sources = "go": without an anchor there is no tone for a sign to point at.

sources

Which resources to query, in order. See details.

max_genes

Stop after this many genes. Drafting is one HTTP call per gene for go and omnipath, so raise it deliberately.

quiet

Suppress progress messages.

Value

A data.frame of drafted rows with w_g, w_g_source, evidence, citation and needs_review, plus an attr(, "unreachable") listing resources that did not respond.

Details

What each resource can and cannot do is worth knowing before you rely on it. go is the only one that gives a gene-to-process sign directly, through positive/negative regulation of X terms, so it needs no path chaining - but its coverage is uneven gene to gene. signor carries explicit gene-to-phenotype rows, with a cell-biological vocabulary that fits metabolic and immune systems better than behavioural ones. omnipath has the broadest coverage and the weakest signs: CollecTRI and DoRothEA, two of its inputs, both document assigning an activating mode BY DEFAULT when they do not know, so a consensus_stimulation at curation_effort = 1 should be read as sign-unknown. trrust is the most honest transcription-factor resource because it emits Unknown rather than guessing.

Nothing returned here is a polarity. It is a proposal, and the needs_review column is TRUE for every row.

Examples

if (FALSE) { # \dontrun{
## Needs network access: each gene is one HTTP call to the chosen resources.
sel <- dmsa_select(systems = "hpa")
draft <- dmsa_polarity_fetch(sel, anchors = list("2" = c("CRH", "POMC")))
utils::write.csv(draft, file.path(tempdir(), "polarity_draft.csv"),
                 row.names = FALSE)
} # }