integrationApp: A Shiny app to integrate GC-FID and GC-MS data

In LucasBusta/phyloChemistry: Chemical and Sequence Analyses in a Phylogenetic Context

Description

A Shiny app to integrate GC-FID and GC-MS data

Usage

integrationApp(chromatograms, x_axis_start = NULL, x_axis_end = NULL,
  samples_monolist_path, create_new_samples_monolist = FALSE,
  samples_monolist_subset, peaks_monolist_path,
  create_new_peak_monolist = FALSE, zoom_and_scroll_rate)

Arguments

chromatograms	A data frame containing columns: "rt", "tic", and "path_to_cdf_csv", which contain retention time, total ion chromatogram intensities, and paths to CDF.csv files generated by the convertCDFstoCSVs function.
x_axis_start	A numeric value for the lower x-axis bounds on the plot generated by the app. Defaults to full length.
x_axis_end	A numeric value for the upper x-axis bounds on the plot generated by the app. Defaults to full length.
samples_monolist_path	A path to a .csv file containing metadata for the samples you wish to analyze. Requied columns are: "rt_offset", "baseline_window", and "path_to_cdf_csv", which are for aligning chromatograms, adjusting baseline determination, and defining the path to the CDF.csv files for each sample, respectively.
samples_monolist_subset	Optional, a numeric vector (for example, "c(1:10)"), defining a subset of samples to be loaded.
peaks_monolist_path	A path to a .csv file containing metadata for all peaks in the sample set. Required columns are: peak_start", "peak_end", "path_to_cdf_csv", "area", "peak_number_within_sample", "rt_offset", "peak_start_rt_offset", "peak_end_rt_offset". This file is automatically generated by the app.
zoom_and_scroll_rate	Defines intervals of zooming and scrolling movement while running the app

LucasBusta/phyloChemistry documentation built on Sept. 6, 2020, 11:36 p.m.