COSMOS (Causal Oriented Search of Multi-Omic Space)

Documentation for package ‘cosmosR’ version 1.19.1

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compress_same_children	Compress Network by Merging Nodes with Identical Children
cosmos_data	Create Cosmos Data
createLinearColors	Create Linear Colors Based on Numeric Input
decompress_moon_result	Decompress Moon Result
decompress_solution_network	Decompress Solution Network
decoupleRnival	DecoupleRnival
default_CARNIVAL_options	Setting Default CARNIVAL Options
display_node_neighboorhood	display_node_neighboorhood
extract_nodes_for_ORA	Extract COSMOS nodes for ORA analysis
filter_incohrent_TF_target	filter_incohrent_TF_target
format_COSMOS_res	format_COSMOS_res
format_LR_ressource	Format Ligand-Receptor Resource
get_moon_scoring_network	Get Moon Scoring Network
gmt_to_dataframe	Convert gmt file to data frame
HMDB_mapper_vec	Toy Input Transcription Data Set
load_tf_regulon_dorothea	load transcription factor regulon
make_heatmap_color_palette	Create Heatmap Color Palette
meta_network	Meta Prior Knowledge Network
meta_network_cleanup	meta_network_cleanup
moon	moon
prepare_metab_inputs	add metabolic compartment and metab__ prefix to metabolite IDs
preprocess_COSMOS_metabolism_to_signaling	Preprocess COSMOS Inputs For Metabolism to Signaling
preprocess_COSMOS_signaling_to_metabolism	Preprocess COSMOS Inputs For Signaling to Metabolism
print.cosmos_data	Print Cosmos Data Summary Print a summary of cosmos data.
reduce_solution_network	reduce_solution_network
reduce_solution_network_double_thresh	reduce_solution_network_double_thresh
run_COSMOS_metabolism_to_signaling	run COSMOS metabolism to signaling
run_COSMOS_signaling_to_metabolism	run COSMOS signaling to metabolism
toy_metabolic_input	Toy Metabolic Input Data
toy_network	Toy Input Network
toy_RNA	Toy Input Transcription Data Set
toy_signaling_input	Toy Signaling Input
translate_column_HMDB	Translate Column Using HMDB Mapper
translate_res	translate_res
wide_ulm_res	Convert ULM Results to Wide Format