Write GMT File — write.gmt • plaid

Write gene sets to GMT file (Gene Matrix Transposed). The GMT format is commonly used to store gene sets or gene annotations.

Usage

write.gmt(gmt, file, source = NA)

Arguments

gmt: A list of gene sets in GMT format: each gene set is represented as a vector of gene names.
file: The file path to write the GMT file.
source: A character vector specifying the source of each gene set. If not provided, the names of the gene sets are used as the source.

Value

Does not return anything.

Examples

# Create example GMT data
gmt <- list(
  "Pathway1" = c("GENE1", "GENE2", "GENE3"),
  "Pathway2" = c("GENE2", "GENE4", "GENE5"),
  "Pathway3" = c("GENE1", "GENE5", "GENE6")
)

# \donttest{
# Write to GMT file (creates file in temp directory)
temp_file <- tempfile(fileext = ".gmt")
write.gmt(gmt, temp_file)

# Write with custom source information
temp_file2 <- tempfile(fileext = ".gmt")
write.gmt(gmt, temp_file2, source = c("DB1", "DB2", "DB3"))

# Clean up
unlink(c(temp_file, temp_file2))
# }