A repo to share with Katherine to review my annotation of targeted compounds in the lab
stan_assignments.R: The main script, used to annotate features with compound names according to rules
- Requires real_peaks.csv, addiso_peaks.csv, and falkor_stans.csv
- Outputs stan_assignments.csv, connects feature numbers to compound names
stan_vis.Rmd: An Rmarkdown document used to visualize the peaks and manually check their annotations
- Requires stan_assignments.csv and stan_data.rds
- Outputs stan_vis.html, a knit document with plotted EICs and metadata.
stan_data_maker.R: Creates stan_data.rds by opening each MS file, extracting relevant data, and formatting. Shouldn't need to be run and will break if run not on Will's computer. Fix the file paths to point to the correct files if you'd like to use this
real_peaks.csv: The list of peaks found by peakpicking, excluding adducts and isotopes
addiso_peaks.csv: The list of peaks found by peakpicking to be adducts or isotopes
falkor_stans.csv: A clean version of the Ingalls Lab Standards sheet
stan_assignments.csv: Data frame associating each standard with a feature number as found by peakpicking
stan_data.rds: A data table with EIC information (mz, rt, int) for each standard to be plotted
stan_vis.html: A knit document with plotted peaks and associated metadata