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basic_network
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Basic Network Object |
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basic_network_interactions
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Basic Network Interactions |
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basic_network_table
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Basic Network Table |
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find_limit()
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Finds the limit cutoff when target and sentinal paths are given |
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genelists
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Sample Genelists to Run Network Functions On |
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list_load()
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Loads a Gene List From Synapse |
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log_into_synapse()
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Log into Synapse |
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name_pull()
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Pull the names of a PathTrace |
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network_load()
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Re-Load the networks and calc meterics |
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path_calc()
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Calculate the OMICS Scores across paths |
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path_filter()
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Filters Paths Baised on OMICS Scores |
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path_obj_filter()
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Finds the limit cutoff when target and sentinal paths are given |
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plot(<igraph2>)
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Modified igraph plotting code to allow for changes in edge.arrow.width.
Edge.arrow.size still not supported
Code provided from: jevansbio/igraphhack
Git User: jevansbio |
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rm_dups()
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Remove Duplicate Gene Entries
The purpose. of this function is to pull info from a synapse table into a
dataframe. Removal can be of all entries with a lower score in a given column
or entries which lack the desired ensg |
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sample_network
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Sample simple network |
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short_paths()
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Traces the shortest paths of a gene to a vector of Target Gene and a vector
of Sentinal Genes |
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sif_boot()
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Load and Add names to SIF formatted files |
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sif_loader()
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Load and Add namees to a list SIF formatted files |
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slim_net
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Test and example network: implicit loading |
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store_net()
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Push Network to Synapse |
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table_pull()
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Pull Synapse Table into Dataframe
The purpose. of this function is to pull info from a synapse table into a
dataframe. |
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trace_filter()
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Process a path trace list |
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vertex_annotate()
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Remove Duplicate Gene Entries
The purpose. of this function is to pull info from a synapse table into a
dataframe. Removal can be of all entries with a lower score in a given column
or entries which lack the desired ensg |