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Read and Process the DDA experiment.

Source: R/dataImport.R
readExperiment.Rd

readExperiment reads and processes DDA (Data-Dependent Acquisition) phosphoproteomic and proteomic data from a given file table, and returns a MultiAssayExperiment object.

Usage

readExperiment(
  fileTable,
  localProbCut = 0.75,
  scoreDiffCut = 5,
  fdrCut = 0.1,
  scoreCut = 10,
  pepNumCut = 1,
  ifLFQ = TRUE,
  annotation_col = c(),
  verbose = FALSE
)

Arguments

fileTable

A data.frame containing information about the input files, including searchType, id, sample, and other annotations.

localProbCut

Numeric, local probability cutoff for filtering phosphoproteomic data. Default is 0.75.

scoreDiffCut

Numeric, score difference cutoff for filtering phosphoproteomic data. Default is 5.

fdrCut

Numeric, false discovery rate cutoff for filtering proteomic data. Default is 0.1.

scoreCut

Numeric, score cutoff for filtering proteomic data. Default is 10.

pepNumCut

Numeric, peptide number cutoff for filtering proteomic data. Default is 1.

ifLFQ

Logical, whether to use LFQ quantification for proteomic data. Default is TRUE.

annotation_col

A character vector specifying additional columns to be included in the sample annotation. Default is an empty vector.

verbose

Logical value indicating whether to print detailed information. Default is FALSE.

Value

A MultiAssayExperiment object containing the processed phosphoproteomic and proteomic data from a DDA experiment.

Details

The function performs the following steps:

  • Reads and processes the phosphoproteomic data using the readPhosphoExperiment function.

  • Reads and processes the proteomic data using the readProteomeExperiment function.

  • Prepares the sample annotation table.

  • Constructs and returns a MultiAssayExperiment object containing the processed data.

Examples

# Example usage:
file1 <- system.file("extdata", "phosDDA_1.xls", package = "SmartPhos")
file2 <- system.file("extdata", "proteomeDDA_1.xls", package = "SmartPhos")
# Create fileTable
fileTable <- data.frame(
  searchType = c("phosphoproteome", "proteome"),
  fileName = c(file1, file2),
  sample = c("Sample1", "sample1"),
  id = c("s1", "s2")
)
# Call the function
readExperiment(fileTable, localProbCut = 0.75, scoreDiffCut = 5,
fdrCut = 0.1, scoreCut = 10, pepNumCut = 1, ifLFQ = TRUE,
annotation_col = c("id"))
#> A MultiAssayExperiment object of 2 listed
#>  experiments with user-defined names and respective classes.
#>  Containing an ExperimentList class object of length 2:
#>  [1] Phosphoproteome: SummarizedExperiment with 2 rows and 1 columns
#>  [2] Proteome: SummarizedExperiment with 2 rows and 1 columns
#> Functionality:
#>  experiments() - obtain the ExperimentList instance
#>  colData() - the primary/phenotype DataFrame
#>  sampleMap() - the sample coordination DataFrame
#>  `$`, `[`, `[[` - extract colData columns, subset, or experiment
#>  *Format() - convert into a long or wide DataFrame
#>  assays() - convert ExperimentList to a SimpleList of matrices
#>  exportClass() - save data to flat files