hptmUsage

Preprocessing, visualization, and analysis (e.g., differential usage) of histone post-translational modifications (hPTMs). This package builds on the ‘msqrob2PTM’ workflow to enable robust and performant analysis of hPTM data.

Installation

Install the development version of hptmUsage from GitHub with:

# Install using "pak", alternatively use `devtools::install_github()` or `renv::install()`
# install.packages("pak")
pak::pak("rualmey/hptmUsage")

This package requires the following software to be installed (and to be found on PATH):

• MAFFT for multiple sequence alignment

• Quarto for reporting of results

Usage

The easiest way to use this package is through the hptmUsage::generateReport() function. A generic workflow is shown below:

library(hptmUsage)

pe <- readProgenesis("./all-peptide-ion-export.csv", generate_metadata = "./metadata.csv")

# Now manually edit the metadata CSV and add it back to the dataset
pe |>
  replaceColData("./metadata.csv") |>
  # And perform the analysis + render the report
  generateReport(
    "./out/",
    # The following contrast will be positive (right side of the volcano) if the usage is higher in group B.
    contrasts = list(factor = c("A vs B" = "groupB - groupA")),
    # Note, if no contrasts are specified, the analysis is still done up to visualizing the design matrix
    # which can help in defining the contrasts
    generate_usageplots = "significant"
    # Note, generating usage plots takes quite some time so only do this once satisfied with the analysis
  )

# You should now be able to find your HTML report under ./out/date_hptmUsage.html

The parameters for hptmUsage::generateReport(), see help("generateReport"), should allow a lot of freedom in how the analysis is performed. Additionally, the fully processed dataset is silently returned from hptmUsage::generateReport(), allowing for easy post-processing.

If, however, more advanced changes to the workflow are required, you can take a look at this basic code example that processes a benchmark dataset, as well as the Quarto report template and the package reference manual.