Write GMT File

Source: R/writeGMT.R

Writes a GMT (Gene Matrix Transposed) file from a data frame.

writeGMT(df, outfile)

Arguments

df

Data frame with columns ordered as Identifiers, optional Name columns and Genes. Identifiers must be first and Genes must be last.
outfile

Path to output GMT file

Value

None

Details

The input data frame must include at least two columns: Identifiers (first column) and Genes (last column). The Identifiers will be duplicated to fill the Name column in the output GMT file. If one or more Name columns are provided in the data frame, #' then they will be concatenated with separators.

References

Adapted from the GMT writer in MAGeCKFlute, https://github.com/WubingZhang/MAGeCKFlute/blob/master/R/readGMT.R

See also

readPathwayGMT

Examples

# \donttest{
my.df <- data.frame(id=c("WP1000","WP1000","WP1000","WP1001","WP1001"),
         name=c("cancer","cancer","cancer","diabetes","diabetes"),
         gene=c("574413","2167","4690","5781","11184"))
writeGMT(my.df, "myGmtFile.gmt")
# }