prepare_gmt_input {mExplorer}

Creation of m:Explorer input data frame from GMT files

Description

Creation of m:Explorer input data frame from GMT files

Usage

prepare_gmt_input(gmt_filename, min_genes = NA, max_genes = NA)

Arguments

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.

Value

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.

Examples

# 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)