R: Analysis of Graph-Structured Data with a Focus on Protein-Protein Interaction Networks

# Analysis of Graph-Structured Data with a Focus on Protein-Protein Interaction Networks

## Documentation for package ‘crosstalkr’ version 1.0.5

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

add_expression | attach expression values from user-provided expression vector to graph.
add_value | Attach a generic user-provided value to graph
as_gene_symbol | Convert from most other representations of gene name to gene.symbol
bootstrap_null | Bootstrap null distribution for RWR
calc_dnp_i | helper function to calculate dnp for one sample
calc_np | calculate network potential for one node.
calc_np_all | function to calculate the network potential for each protein in a user-provided vector - cpp internal version
calc_np_all_legacy | function to calculate the network potential for each protein in a user-provided vector
calc_np_i | helper function to calculate np for one sample
check_crosstalk | Check to make sure incoming object is a valid crosstalk df.
combine_null | .combine function for compute_null foreach looping structure
compute_crosstalk | Identify proteins with a statistically significant relationship to user-provided seeds.
compute_dnp | main function to compute delta np for every gene in a given dataframe - assumes compute_np has already been run for a given dataset
compute_np | main function to compute np from a user-provided expression matrix.
compute_null_dnp | function to compute null distribution of dnp
crosstalkr | crosstalkr: A package for the identification of functionally relevant subnetworks from high-dimensional omics data.
crosstalk_subgraph | Helper function to generate subgraph from crosstalk_df output of 'compute_crosstalk'
detect_inputtype | Determine which format of gene is used to specify by user-defined seed proteins
dist_calc | Internal function that computes the mean/stdev for each gene from a wide-format data frame.
ensembl_type | Determine if ensembl id is a Protein, gene, or transcript_id
experiment_breakout | helper function to split experiment names into constituent parts
fcalc_np_all | Function to calculate the network potential for vertices v
final_combine | final .combine function to run in compute_null_dnp foreach looping structure
final_dist_calc | Internal function that computes the mean/stdev for each gene from a wide-format data frame.
get_neighbors | function to get graph neighbors (along with their expression values) for a given gene in a given network g
get_random_graph | Helper function for compute_null_dnp - returns a graph with randomly permuted edges.
get_topn | Helper function for compute_null_dnp - returns the top n genes by dnp for each sample
gfilter | Generic function to filter either an igraph object or a PPI network
gfilter.ct | Method to filter the graph based on parameters passed to compute_crosstalk
gfilter.igraph_method | Method to filter graph based on any igraph method that scores verticies.
gfilter.np | Method to filter graph based on network potential values.
gfilter.value | Method to filter graph based on user provided value
is_ensembl | Determine if a character vector contains ensembl gene_ids
is_entrez | Determine if a character vector contains entrez gene_ids
load_ppi | Helper function to load requested PPI w/ parameters
match_seeds | Identify random sets of seeds with similar degree distribution to parent seed proteins
node_repression | Function to eliminate a node from a network g and calculate the change in some measure of network state
norm_colsum | Function to normalize adjacency matrix by dividing each value by the colsum.
plot_ct | Plot subnetwork identified using the compute_crosstalk function
ppi_intersection | Function to allow users to choose the intersection of stringdb and biogrid Only works with the human PPI. min_score parameter only applies to strindb
ppi_union | Function to allow users to choose the union of stringdb and biogrid Only works with the human PPI. min_score parameter only applies to strindb
prep_biogrid | Prepare biogrid for use in analyses
prep_stringdb | Prepare Stringdb for use in analyses
sparseRWR | Perform random walk with repeats on a sparse matrix
supported_species | returns a dataframe with information on supported species
tidy_expression | helper function to convert expression matrix to tidy dataframe (if not already)
to_taxon_id | helper to convert user-inputs to ncbi reference taxonomy.