SilacPeptideExperiment-constructor {pulsedSilac} | R Documentation

## SilacPeptideExperiment constructor

### Description

Constructor function for the SilacPeptideExperiment class object.

### Usage

    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

    ## 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')

[Package pulsedSilac version 1.1.4 Index]