[Anshuman] Create GroupComparisonQCPlots

[tonywu1999]

Context

The linear mixed effects models that MSstats uses assume constant variance among its residuals. However, in MS-based proteomics, the distribution of intensity values tends to be right-skewed, which can lead to residuals of a linear mixed effects model being right-skewed (violating the constant variance assumption). As a result, MSstats applies log transformation on intensities in order to transform those values from a right-skew distribution to a normal distribution, leading to a better fit model.

New Subtasks

• Look into source code in groupComparisonPlots
• Look into source code of qqPlot in envStats
• Write R code to generate QQ plots based on the residuals of the model using groupComparisonPlots
  • User input: protein ID / all
    • all would make a QQ plot for each protein ID
  • Color by condition (secondary)
• Unit Test
• PR & Merge

Acceptance Criteria

QQ plots have been generated

[tonywu1999]

If making a singular QQ plot for all proteins, one idea was to standardize residuals (by dividing residuals by sample variance of the linear model) and overlay to see if the extra insight is valuable.

[tonywu1999]

New subtasks - apparently there is a function called modelBasedQCPlots that does this already

• Add groupComparisonQCPlots function that wraps modelBasedQCPlots
• Rename file to groupComparisonQCPlots.R
• Add deprecation message if someone uses modelBasedQCPlots directly
• Unit test the wrapper (testhat + mockery)
• Add to vignette
• PR & Merge