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

Description Usage Arguments Value Class description Accessors Examples

Constructor function for the SilacProteinExperiment class object.

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

`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...

An object of class SilacProteinExperiment.

See SilacProteinExperiment-class for details.

See SilacProteinPeptideExperiment-accessors for details.

## 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')