SilacPeptideExperiment-constructor: SilacPeptideExperiment constructor

Description Usage Arguments Value Class description Accessors Examples

Description

Constructor function for the SilacPeptideExperiment class object.

Usage

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SilacPeptideExperiment(
  assays,
  rowData = NULL,
  colData = NULL,
  conditionCol = NA,
  timeCol = NA,
  proteinCol = NA,
  metadata = NULL
)

Arguments

assays

A named list of matrices (assays) with peptide level data.

rowData

A data.frame with peptide feature data like protein names, molecular weight, etc.

colData

A data.frame with sample information like conditions, replicates, etc.

conditionCol

A character, which indicates the column name in colData(x) that defines the different experiment conditions.

timeCol

A character, which indicates the column name in colData(x) that defines the different experiment timepoints.

proteinCol

A character, which indicates the column name in rowData(x) that defines to which protein a peptide is assigned.

metadata

A list to store any kind of experiment-wide data; like authors, dates, machines used...

Value

An object of class SilacPeptideExperiment.

Class description

See SilacPeptideExperiment-class for details.

Accessors

See SilacProteinPeptideExperiment-accessors for details.

Examples

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## assays
assays_peptide <- list(expression = matrix(1:15, ncol = 3))

## colData
colData <- data.frame(sample = c('A1', 'A2', 'A3'),
                      condition = c('A', 'A', 'A'),
                      time = c(1, 2, 3))
## rowData
rowData_peptide <- data.frame(pept_id = letters[1:5],
                              prot_id = c('A', 'A', 'B', 'C', 'C'))
## construct the ProteinExperiment
peptExp <- SilacPeptideExperiment(assays = assays_peptide,
                                  rowData = rowData_peptide,
                                  colData = colData,
                                  conditionCol = 'condition',
                                  timeCol = 'time')

pulsedSilac documentation built on Nov. 8, 2020, 5:13 p.m.