summarize_ptmProteins: Summarize modified peptides and modification sites per...

In nicohuttmann/ptmOmics: Post-translational modifications add-on for pOmics

Summarize modified peptides and modification sites per proteinGroup

Description

Summarize modified peptides and modification sites per proteinGroup

Usage

summarize_ptmProteins(
  proteinGroups,
  modificationSpecificPeptides,
  sites,
  observations,
  replicates = "groups",
  replicates.min = 2/3,
  group.by = "cell.line",
  modification = "Phospho (STY)",
  modification.abbr = "p",
  min.localization.prob = 0.75,
  add.info = c("Gene.names", "Protein.names")
)

Arguments

proteinGroups	proteinGroups
modificationSpecificPeptides	modificationSpecificPeptides
sites	sites
observations	observations
replicates	observations data for biological replicates etc.
replicates.min	min fraction to be considered identified
group.by	observatrions data to groups by
modification	name of modification site dataset
modification.abbr	abbreviation to use for modification (e.g. 'p')
min.localization.prob	localization probability threshold (e.g. 0.75)

nicohuttmann/ptmOmics documentation built on Nov. 9, 2022, 4:01 a.m.