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Read and Process a DIA Experiment

Source: R/dataImport.R
readExperimentDIA.Rd

readExperimentDIA reads and processes DIA (Data-Independent Acquisition) data for both phosphoproteome and proteome experiments, and constructs a MultiAssayExperiment object.

Usage

readExperimentDIA(
  fileTable,
  localProbCut = 0.75,
  annotation_col = c(),
  onlyReviewed = TRUE,
  normalizeByProtein = FALSE,
  verbose = FALSE
)

Arguments

fileTable

A data frame containing metadata about the files to be read. Must contain columns searchType, fileName, id, and optionally outputID.

localProbCut

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

annotation_col

A character vector specifying the columns in fileTable to be used for sample annotation.

onlyReviewed

A logical value indicating whether to include only reviewed proteins. Default is TRUE.

normalizeByProtein

Logical, whether to normalize the data by protein. Default is FALSE.

verbose

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

Value

A MultiAssayExperiment object containing the processed phosphoproteome and proteome data.

Details

The function performs the following steps:

  • Reads and processes phosphoproteomic data using readPhosphoExperimentDIA.

  • Reads and processes proteomic data using readProteomeExperimentDIA.

  • Prepares sample annotations based on the provided fileTable and annotation_col.

  • Constructs a MultiAssayExperiment object with the processed data and sample annotations.

The readPhosphoExperimentDIA and readProteomeExperimentDIA functions are used to read and filter the data for phosphoproteome and proteome experiments, respectively, and they must be available in the environment.

Examples

# Example usage:
file1 <- system.file("extdata", "phosDIA_1.xls", package = "SmartPhos")
file2 <- system.file("extdata", "proteomeDIA_1.xls", package = "SmartPhos")
# Create fileTable
fileTable <- data.frame(
  searchType = c("phosphoproteome", "proteome", "proteome"),
  fileName = c(file1, file2, file2),
  id = c("Sample_1", "sample1", "sample2"),
  outputID = c("s1", "s2", "s3")
)
# Call the function
readExperimentDIA(fileTable, localProbCut = 0.75, annotation_col = c("id"),
onlyReviewed = FALSE, normalizeByProtein = FALSE)
#> 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 2 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