using query_missingGenes_from_module on multiple modules about metqy HOT 3 OPEN

library(Metqy)
# install.packages('reshape2')

data("data_example_KOnumbers_vector")
modules <- c('M00001', 'M00002')

module_missing_genes_str <- data.frame('MODULE' = modules,
                                   'MISSING_GENES' = '',
                                   stringsAsFactors = FALSE)

# Collect pairs of modules and each missing gene by constructnig the following structure:
#
#   MODULE  MISSING_GENE
#   M00001 K00001
#   M00001 K00002
#   M00001 K00003
#   M00002 K00004
module_missing_genes_pairs <- NULL
  

for(M in 1:length(modules)){
  OUT <- query_missingGenes_from_module(data_example_KOnumbers_vector,modules[M])
  these_genes_list <- OUT$MISSING_GENES
  # collapse list into string
  these_genes_str <- paste(these_genes_list, collapse=',')
  module_missing_genes_str$MISSING_GENES[M] <- these_genes_str
  
  # Append the combination of the module ID repeted as many times as there are missing genes 
  #                             combine rows together
  module_missing_genes_pairs <- rbind(module_missing_genes_pairs,
                                      # combine two list into pair-wise columns
                                      cbind(rep(modules, length(these_genes_list)), these_genes_list))
  
}
# Tiddy module_missing_genes_pairs up 
module_missing_genes_pairs <- data.frame(module_missing_genes_pairs, stringsAsFactors = FALSE)
names(module_missing_genes_pairs) <- c('MODULE', 'MISSING_GENES')

# GENERATE A MATRIX OF THE MODULES AND THE MISSING GENES WHERE '1' INDICATES THE GENE IS MISSING FOR THAT MODULE
module_missing_genes_pairs$Value <- 1
module_missing_genes_matrix <- reshape2::dcast(module_missing_genes_pairs,formula = MODULE~MISSING_GENES,value.var = "Value",drop = F,fill = 0)
# Use the module ID to name the rows
rownames(module_missing_genes_matrix) <- module_missing_genes_matrix[,1]
# Remove the colums with the module IDS to have a numeric matrix

module_missing_genes_matrix           <- module_missing_genes_matrix[,2:ncol(module_missing_genes_matrix)]