SilacProteinExperiment-constructor {pulsedSilac} | R Documentation

## SilacProteinExperiment constructor

### Description

Constructor function for the SilacProteinExperiment class object.

### Usage

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

### Arguments

`assays` | A named `list` of matrices (assays) with protein level data.
`rowData` | A `data.frame` with protein 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.
`metadata` | A `list` to store any kind of experiment-wide data; like authors, dates, machines used...

### Value

An object of class `SilacProteinExperiment`.

### Class description

See SilacProteinExperiment-class for details.

### Accessors

See SilacProteinPeptideExperiment-accessors for details.

### Examples

    ## assays
    assays_protein <- list(expression = matrix(1:9, ncol = 3))

    ## colData
    colData <- data.frame(sample = c('A1', 'A2', 'A3'),
                          condition = c('A', 'A', 'A'),
                        time = c(1, 2, 3))
    ## rowData
    rowData_protein <- data.frame(prot_id = LETTERS[1:3])

    ## construct the ProteinExperiment
    protExp <- SilacProteinExperiment(assays = assays_protein,
                                      rowData = rowData_protein,
                                      colData = colData,
                                      conditionCol = 'condition',
                                      timeCol = 'time')

[Package pulsedSilac version 1.6.0 Index]