Workflow for MaxQuant data analysis — workflow

The purpose of this function is to provide a single function that will take a proteinGroups.txt produced by MaxQuant, perform the necessary data processing, and generate a volcano plot. This function will call the load_maxquant(), process_maxquant(), and volcano_plot_maxquant() functions in turn. The user will be asked to specify which groups are group 1 or group 2.

Usage

workflow_maxquant(...)

Arguments

...

ellipsis to allow the user to specify arguments for each function in the workflow. The accepted arguments for each function are as follows:

load_maxquant(): file, datadir, clean
process_maxquant(): group1, group2, meas, baseval, width, downshift, seed, var.equal, paired
volcano_plot_maxquant(): meas, threshold_p, threshold_fc, p_line, zero_line, x_line, vp_colours, groups, x_label, y_label, fsize

Value

A ggplot object containing the volcano plot generated from the MaxQuant data.

Examples

if (FALSE) { # \dontrun{
workflow_maxquant()
} # }