proteusData: 'proteusData' constructor
In bartongroup/Proteus: Downstream analysis of the MaxQuant output

proteusData

R Documentation

`proteusData` constructor

Description

proteusData constructor

Usage

proteusData(
  tab,
  metadata,
  content,
  pep2prot,
  peptides,
  proteins,
  measures,
  npep = NULL,
  type = "label-free",
  sequence.col = "sequence",
  protein.col = "protein",
  peptide.aggregate.fun = NULL,
  peptide.aggregate.parameters = NULL,
  protein.aggregate.fun = NULL,
  protein.aggregate.parameters = NULL,
  min.peptides = NULL,
  norm.fun = identity
)

Arguments

`tab`	A matrix with data, rows are peptides/proteins, columns are samples
`metadata`	A data frame with metadata, needs at least two columns: "sample" and "condition"
`content`	Either "peptides" or "proteins"
`pep2prot`	A data frame with two columns: "sequence" and "protein". Can use "other" for non-proteus data.
`peptides`	A character vector with peptide sequences
`proteins`	A character vector with protein names
`measures`	A character vector with names of intensity and/or ratio columns
`npep`	A data frame with number of peptides per protein
`type`	Type of experiment: "label-free" or "SILAC"
`sequence.col`	Name of the sequence used, either "sequence" or "modified_sequence"
`protein.col`	Name of the protein column used, either "protein" or "protein_group"
`peptide.aggregate.fun`	Function used to aggregate peptides
`peptide.aggregate.parameters`	Additional parameters passed to peptide aggregate function
`protein.aggregate.fun`	Function used to aggregate proteins
`protein.aggregate.parameters`	Additional parameters passed to protein aggregate function
`min.peptides`	Integer, minimum number of peptides to combine into a protein
`norm.fun`	Normalizing function