This repository contains Daniel Golden's R scripts used in the completion of the analyst roles for projects 2 and 3 for the individual project final of BF528.
In this project, I have completed the tasks associated with the analyst role in projects 2 and 3, analyzing either instructor-provided data or programmer-generated data associated with data analysis in the recreation of the results reported by O'Meara et al. and Wang et al.
All that is required to generate the plots and data for the analyst role in project 2 is to open the following .R file in Rstudio, substitute the filepath used in the script to read in the gene_exp.diff file with the filepath for that file locally stored on the user's computer (or the following filepath if Rstudio is being run on the SCC: "/project/bf528/project_2/data/P4_vs_P7_cuffdiff_out/gene_exp.diff"), and run the script.
BF528_final_omeara_analyst.R
All that is required to generate the plots and data for the analyst role in project 3 is to open the following .R file in Rstudio, substitute the filepaths used in the script to read in the RMA expression matrix and toxgroup 6 metadata with the filepaths for those files locally stored on the user's computer (or the following filepaths if Rstudio is being run on the SCC: "/project/bf528/project_3/samples/liver-normalization-rma.txt" and "/project/bf528/project_3/groups/group_6_mic_info.csv"), and run the script.
BF528_final_wang_analyst.R