The enclosed .R files were developed using R 3.4.2.
Place the .R files in your working directory. Also place the uncompressed text
files BIOGRID-ORGANISM-Homo_sapiens-3.1.91.tab and gene_association.goa_human
in your working directory (NOTE: do not have the .txt extension on the file names).
Run 'source("midterm.R")' in the R console. The script will read in the files
build a lookup table. You will be asked to supply a protein name. The script
will take the input and find the GO id that is most associated with that
protein in the interactions file. A data frame is returned with the GO id,
the number of protein interactions that GO id was found in, and descriptive
information from the Amigo website (http://amigo.geneontology.org/amigo).
If there is a tie in the maximum number of GO ids for the protein, then
the data frame will have more than one record. If the protein isn't recognized,
then the returned text says it can't match the protein with the list of
Official Symbols. If the maximum number of interactions for a GO id is 1,
then the returned text says there is not enough information to associate
a function.
After a protein is submitted and a function is returned, you will be asked
if you would like to start a shiny app. If you type 'y' and hit enter,
a shiny app will open in your default browser. You will be able to select
proteins from a list and see the returned function as a table in the browser.
You can also see the app here: https://natebyers.shinyapps.io/B573midterm/.