Handle Ambiguity of Protein Identifications from Shotgun Proteomics

Documentation for package ‘net4pg’ version 0.1.1

cc_composition	Get peptides and peptide-to-protein mappings for each connected component
cc_stats	Provide statistics on the CCs size
get_adj_matrix	Generate adjacency matrix
get_cc	Generate graph and calculate its connected components
peptide_stats	Calculate percentage of shared vs specific peptides
plot_cc	Plot peptide-to-protein mapping graph
read_inc_matrix	Read incidence matrix of proteomic identifications
reduce_inc_matrix	Reduce size of incidence matrix for downstream analyses
transcriptome_filter	Perform transcriptome-informed post-hoc filtering