SilacProteomicsExperiment-constructor {pulsedSilac} | R Documentation

## SilacProteomicsExperiment constructor

### Description

Constructor function for the ProteomicsExperiment class object. It requires at minimum a `SilacProteinExperiment` and a `SilacPeptideExperiment`. If the colData, metadata and metaoptions have been already defined in those it is not necessary to give them again.

### Usage

    SilacProteomicsExperiment(
      SilacProteinExperiment,
      SilacPeptideExperiment,
      colData,
      linkerDf,
      metadata,
      idColProt = NA,
      idColPept = NA,
      linkedSubset = TRUE,
      subsetMode = "protein",
      conditionCol = NA,
      timeCol = NA,
      proteinCol = NA
    )

### Arguments

`SilacProteinExperiment` | A `SilacProteinExperiment` object.
`SilacPeptideExperiment` | A `SilacPeptideExperiment` object.
`colData` | A `data.frame` with sample information like conditions, replicates, etc. If not provided uses the colData slot from the `SilacProteinExperiment` and `SilacPeptideExperiment`.
`linkerDf` | A `data.frame` output from `buildLinkerDf`.
`metadata` | A `list` to store any kind of experiment-wide data; like authors, dates, machines used... If not provided uses the metadata from the `SilacProteinExperiment` and `SilacPeptideExperiment`.
`idColProt` | A `character` indicating which column from the rowData (protein) should be used as ids. Should be the same used in `buildLinkerDf`.
`idColPept` | A `character` indicating which column from the rowData (peptide) should be used as ids. Should be the same used in `buildLinkerDf`.
`linkedSubset` | A `logical` if subsetting should be linked between proteins and peptide.
`subsetMode` | A `character`, either 'protein' or 'peptide' indicating which level should be used first when subsetting.
`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.

### Value

An object of class `SilacProteomicsExperiment`.

### Class description

See SilacProteomicsExperiment-class for details.

### Accessors

See SilacProteomicsExperiment-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')

    ## 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')

    ## list with the relationships
    protein_to_peptide <- list(A = c('a', 'b'), B = c('c'), C = c('d', 'e'))
    ## function to build the data.frame
    linkerDf <- buildLinkerDf(protIDs = LETTERS[1:3],
                              pepIDs  = letters[1:5],
                              protToPep = protein_to_peptide)

    ProteomicsExp <- SilacProteomicsExperiment(SilacProteinExperiment = protExp,
                                               SilacPeptideExperiment = peptExp,
                                               linkerDf = linkerDf)

[Package pulsedSilac version 1.8.0 Index]