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

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Documentation for package ‘crosstalkr’ version 1.0.5

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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.