build_binary_matrix: Build binary presence/absence matrix of sporulation genes

In SpoMAG: Probability of Sporulation Potential in MAGs

Build binary presence/absence matrix of sporulation genes

Description

Transforms the output of sporulation_gene_name() into a wide-format matrix indicating the presence (1) or absence (0) of each sporulation-associated gene per genome.

Usage

build_binary_matrix(df)

Arguments

df	A data.frame from sporulation_gene_name() with columns genome_ID and spo_gene_name.

Value

A wide-format binary matrix with genomes in rows and genes in columns.

Examples

# Load package
library(SpoMAG)

# Load example annotation tables
file_spor <- system.file("extdata", "one_sporulating.csv.gz", package = "SpoMAG")
file_aspo <- system.file("extdata", "one_asporogenic.csv.gz", package = "SpoMAG")

# Read files
df_spor <- readr::read_csv(file_spor, show_col_types = FALSE)
df_aspo <- readr::read_csv(file_aspo, show_col_types = FALSE)

# Step 1: Extract sporulation-related genes
genes_spor <- sporulation_gene_name(df_spor)
genes_aspo <- sporulation_gene_name(df_aspo)

# Step 2: Convert to binary matrix
bin_spor <- build_binary_matrix(genes_spor)
bin_aspo <- build_binary_matrix(genes_aspo)

SpoMAG documentation built on June 8, 2025, 1:48 p.m.