generateBipartiteGraph: Generate a Graph based on Peptide and Protein

In kairenchen721/interpretproteinidentification: Visually Interprets Protein Identification

Description

Based on the protein that can be mapped to peptide which are identified from mass spectrometry, a bipartite graph, is drawn.

Usage

generateBipartiteGraph(peptideProteinEdgeVector, inferredProteinVector)

Arguments

peptideProteinEdgeVector	A mapping of protein accession to peptide sequence in a character vector, either the odd elements are all proteins and the even elements are all peptide or the odd elements are all peptides and the even elements are all proteins. There should be an even number of elements
inferredProteinVector	A character vector of all protein that are inferred (that is considered presented in the pre mass spectrometry sample) out of all possible proteins

Details

It takes a mapping of protein accession to peptide sequence, which is then used by function from the igraph package to generate the graph, then decompose into weakly connected components. This un-directed bipartite graph consist of a set of vertices that represent proteins and a set of vertices that represent peptides. The edges between protein vertices and peptide vertices represent protein-peptide matches. Protein accession, peptide identifiers will be displayed at this layer.

Value

It will return a igraph object that include all mapping of protein to peptides

References

Csardi G, Nepusz T (2006). The igraph software package for complex network research. InterJournal, Complex Systems, 1695. https://igraph.org.

Examples

generateBipartiteGraph(allEdges)

dbPath <- system.file("extdata", "test_data.osw", package = "interpretproteinidentification")
otherEdges <- readSQLiteFile(dbPath)
generateBipartiteGraph(otherEdges)

kairenchen721/interpretproteinidentification documentation built on Dec. 21, 2021, 5:15 a.m.