SilacPeptideExperiment-constructor: SilacPeptideExperiment constructor
In pulsedSilac: Analysis of pulsed-SILAC quantitative proteomics data

Description Usage Arguments Value Class description Accessors Examples

Constructor function for the SilacPeptideExperiment class object.

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

`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...

An object of class SilacPeptideExperiment.

See SilacPeptideExperiment-class for details.

See SilacProteinPeptideExperiment-accessors for details.

## 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')