selectProtein: Display a Protein/Peptide and Its Neighbors

In kairenchen721/interpretproteinidentification: Visually Interprets Protein Identification

Description

select a protein and all the peptide that it maps to or a peptide and all the proteins that it maps to, to display. This function expect the output of generateBipartiteGraph and displayComponent to be its input.

Usage

selectProtein(graphToSearchIn, vertexIdentifier)

Arguments

graphToSearchIn	is the component that the user has chosen to displayed in displayComponent, selectProtein searches within this component
vertexIdentifier	is an identifier for the vertex in the graph, so what this refers to here would be either a protein accession or peptide sequence

Details

Using igraph function, It first finds the vertex object that identifier refers to, then find the neighbors of that vertex, and finally induce a sub-graph that include them. When this subgraph is plotted, if the vertexIdentifier is a protein accession, the gene ontology IDs will be display at the top of the plot, if it is involve in disease then it will be displayed at the bottom. (if it is not, then nothing would be displayed). Also to display all the neighbour of a protein/peptide is to plot what peptide/protein can be mapped to the vertex in question from vertexIdentifier

Value

The sub-graph that include a vertex and all its neighbors, the list of gene ontology IDs, and a list of involved diseases (if there is one)

References

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

Examples

wholeGraph <- generateBipartiteGraph(allEdges)
oneComponent <- displayComponent(wholeGraph, 1)
selectProtein(oneComponent, "P02769")
selectProtein(wholeGraph, "P02769")
selectProtein(oneComponent, "DDSPDLPK")
selectProtein(wholeGraph, "DDSPDLPK")

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