Description Usage Arguments Value Examples
Creation of m:Explorer input data frame from GMT files
1 | prepare_gmt_input(gmt_filename, min_genes = NA, max_genes = NA)
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gmt_filename |
Path to GMT file to convert. |
min_genes |
Numeric indicating to discard pathways with less than min_genes genes. If NA, there is no lower bound on the number of genes. Default is NA. |
max_genes |
Numeric indicating to discard pathways with more than max_genes genes. If NA, there is no upper bound on the number of genes. Default is NA. |
Data frame with pathways as columns, genes as rows. Gene/pathway combinations are marked with "pw" if that gene is in the pathway, or "." if not.
1 2 3 4 | # Create m:Explorer input data frame from GMT "small_gmt.gmt," discarding
# pathways with less than 5 genes and more than 1000 genes
gmt_file = system.file("extdata", "small_gmt.gmt", package = "mExplorer")
gmt = prepare_gmt_input(gmt_file, 5, 1000)
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