sporulation_gene_name: Identify Sporulation-Associated Genes

In SpoMAG: Probability of Sporulation Potential in MAGs

Identify Sporulation-Associated Genes

Description

This function identifies sporulation-associated genes in a genome annotation data frame. It searches for gene names and KEGG Orthology identifiers related to sporulation steps and returns a data frame with annotated sporulation genes and a consensus name.

Usage

sporulation_gene_name(df)

Arguments

df	A data frame containing MAG annotation with the columns 'Preferred_name', 'KEGG_ko', and 'genome_ID'.

Value

A data frame of sporulation-associated genes with standardized names and spo_process tags.

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)

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