This function checks if an annotation table meets the required format for metabolite annotation. It verifies the presence of necessary columns, data types, and ensures that no critical values are missing (NA).
Value
The function returns a message indicating that the annotation_table meets the required format, or it stops with an error message if any checks fail.
Examples
# Create a valid annotation table
annotation_table <- data.frame(
variable_id = c("feature1", "feature2"),
ms2_files_id = c("file1", "file2"),
ms2_spectrum_id = c("spec1", "spec2"),
Compound.name = c("Glucose", "Fructose"),
CAS.ID = c("50-99-7", "57-48-7"),
HMDB.ID = c("HMDB0000122", "HMDB0000660"),
KEGG.ID = c("C00031", "C00095"),
Lab.ID = c("Lab001", "Lab002"),
Adduct = c("[M+H]+", "[M+Na]+"),
mz.error = c(0.001, 0.002),
mz.match.score = c(0.95, 0.96),
RT.error = c(0.1, 0.2),
RT.match.score = c(0.9, 0.92),
CE = c(20, 30),
SS = c("MS2_001", "MS2_002"),
Total.score = c(0.85, 0.88),
Database = c("HMDB", "KEGG"),
Level = c("Level 1", "Level 2"),
stringsAsFactors = FALSE
)
# Validate the table
check_annotation_table(annotation_table)