interpretProteinIdentitification: interpretProteinIdentitification: A package for visualizing...

In kairenchen721/interpretproteinidentification: Visually Interprets Protein Identification

Description

The interpretProteinIdentitification package provides foir functions: readSQLiteFile, generateBipartiteGraph, displayComponent, selectProtein

readSQLiteFile function

This function take an OSW file (SQL database file) and return a a mapping of protein accession to peptide sequence,

generateBipartiteGraph function

The generateBipartiteGraph function take in a mapping of protein accession to peptide sequence, files and make a graph

displayComponent function

The displayComponent function take in graph object generated by generateBipartiteGraph and plot one of it components

selectProtein function

The selectProtein function take in any graph object (either the whole graph from generateBipartiteGraph or a component from displayComponent) and display only the portion of the graph/component that is connect to the inputted protein

Reason of separating generateBipartiteGraph and displayComponent

The reason why generateBipartiteGraph and displayComponent is separate because there may be more than 1 component that the user want to look at, if the package were to make displayComponent as a helper function to generateBipartiteGraph, and have the user input a integer as a argument to generateBipartiteGraph, this may cause 3 problems. The first one is that if displayComponent functionality is only in generateBipartiteGraph is that every time the user needs to display another component, the package re-generate the whole graph again, which can be very resource intensive. The second one is that if displayComponent functionality also exist as a separate user-facing function, is that the user may get confused and re-generate the whole again regardless. The third one is that in either case, we have an additional parameter, while it may not be an really bad thing, it is may be better to avoid having more parameters.

what this package is going to need

There are only 4 pieces of data that my package needs.

1. The protein’s accession number 2. Protein-peptide matches (this just means which peptide’s sequence matches part of the protein sequence). 3. An identifier for the peptides. 4. The protein that are“identified”, meaning that they are considered present in the sample. It assumed that there are all in osw files. Sometimes, there is a data for “before” protein inference and data for “after” protein inference. sometimes, the “after” may not provide the peptides so this package will also assume that both “before” and “after” files will be provided

Error causing roxygen tag

I am not sure why the error appears, but once I include the 2 roxygen tag that calling usethis::use_rcpp() tell to add, load_all, document, clean and rebuild all have the same error, the error persist even if it remove the tags, so I am not including them here

About Reticulate

figuring out why reticulate is not working took me so long so I did not have as much time as I would have to develop this package (It ended up not working)

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