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Build presence/absence matrix from clustering results

Source: R/matrix.R
build_pa_matrix.Rd

Creates a matrix with orthogroups as rows and assemblies as columns. Can produce binary (0/1), score-based, or count matrices.

Usage

build_pa_matrix(
  orthogroups,
  proteins = NULL,
  type = "binary",
  score_column = "custom_score",
  score_threshold = NULL,
  score_aggregation = "max",
  exclude_singletons = FALSE
)

Arguments

orthogroups

An orthogroup_result object.

proteins

Optional protein_collection with score data.

type

Character. Matrix type: "binary", "count", or "score".

score_column

Character. Column name for scores (default: "custom_score").

score_threshold

Numeric. Only include proteins with score >= threshold.

score_aggregation

Character. How to aggregate scores: "max", "mean", or "sum".

exclude_singletons

Logical. If FALSE (default), singletons are included as single-member orthogroups with IDs like "OG_single_001". If TRUE, singletons are excluded from the matrix.

Value

A pa_matrix object.

Examples

if (FALSE) { # \dontrun{
pa <- build_pa_matrix(clusters)
pa <- build_pa_matrix(clusters, score_threshold = 5.0)
pa <- build_pa_matrix(clusters, exclude_singletons = TRUE)
} # }