correct_PTM_by_Protein — correct_PTM_by

Adjust modified-enrich peptide quantities (PTM relative proteomics) by a relative global proteomics data via matching correct_key and correct_level

Usage

correct_PTM_by_Protein(
  enriched_peptide,
  relative_protein,
  correct_key = c("name", "ID"),
  correct_level = c("condition", "replicate"),
  unidentified_treatment = c("retain", "remove")
)

Arguments

enriched_peptide: The SummarizedExperiment object of modified-relative proteomics.
relative_protein: The SummarizedExperiment object of the relative global proteomics
correct_key: The key identifier column to match PTM peptides and proteins, one of "name", "ID"
correct_level: Character(1), how to match experiment design, should be one of "condition" or "replicate"
unidentified_treatment: Character(1), one of "retain", "remove", how to treat the PTM peptides whose proteins are unidentified in the relative global proteomics

Value

A modified-relative proteomics SummarizedExperiment object with adjusted quantities