Project: s41467-025-59404-y | Function: fun_modseq_diannMQlib2pSTY (r)

system: You are an expert R programmer implementing algorithms from scientific papers.
Complete the masked function based on the algorithm description.
Follow R best practices and maintain consistent code style.
Return **only** the complete R function code.

user: Complete this R function:

**DESCRIPTION:** Phosphopeptide sequence modification processing. Converts phosphorylation modifications to standardized pS, pT, pY notation and removes SILAC labels and other modification tags.

**KEY TERMS:** {
  "seq_p": "phosphopeptide sequence",
  "pS/pT/pY": "phosphorylated serine/threonine/tyrosine",
  "SILAC": "stable isotope labeling"
}

**CONTEXT CODE:**     # Package not available
  } else {
    library(tidyverse)
  }
  if (!requireNamespace("data.table", quietly = TRUE)) {
    # Package not available
  } else {
    library(data.table)
  }
  if (!requireNamespace("patchwork", quietly = TRUE)) {
    # Package not available
  } else {
    library(patchwork)
  }
  if (!requireNamespace("limma", quietly = TRUE)) {
    # Package not available
  } else {
    library(limma)
  }
  if (!requireNamespace("ggrepel", quietly = TRUE)) {
    # Package not available
  } else {
    library(ggrepel)
  }
  if (!requireNamespace("stringr", quietly = TRUE)) {
    # Package not available
  } else {
    library(stringr)
  }
})

#---------------------------
# Define Directories
#---------------------------
# Wrap global code to prevent execution during testing
if (FALSE) {
  results_dir <- "Results"
  data_dir    <- "Data"
  plots_dir   <- "Plots"

  if (!dir.exists(results_dir)) dir.create(results_dir, recursive = TRUE)
  if (!dir.exists(data_dir))    dir.create(data_dir, recursive = TRUE)
  if (!dir.exists(plots_dir))   dir.create(plots_dir, recursive = TRUE)
}  # End of disabled global code


#---------------------------
# Custom Functions
#---------------------------

fun_modseq_diannMQlib2pSTY <- function(seq_p) {
  stop("Function implementation has been masked")
}


Complete the function implementation replacing "stop("Not implemented")".