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Read and Process a DIA Proteome Experiment

Source: R/helper.R
readProteomeExperimentDIA.Rd

readProteomeExperimentDIA reads and processes DIA (Data-Independent Acquisition) proteome data from multiple files and constructs a SummarizedExperiment object.

Usage

readProteomeExperimentDIA(fileTable, showProgressBar = FALSE)

Arguments

fileTable

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

showProgressBar

Logical, whether to show a progress bar during processing. Default is FALSE.

Value

A SummarizedExperiment object containing the processed proteome data. #' @details The function performs the following steps:

  • Filters the `fileTable` to include only rows where `searchType` is "proteome".

  • For each file specified in `fileTable`, reads the data using `data.table::fread`.

  • Removes rows where the `PG.ProteinGroups` column is NA or empty.

  • Processes each sample in parallel using `BiocParallel::bplapply`, applying the `readOneProteomDIA` function to filter and clean the data for each sample.

  • Combines the processed data from all files.

  • Constructs a matrix of intensities with rows corresponding to proteins and columns corresponding to samples.

  • Constructs a `SummarizedExperiment` object with the intensity matrix and protein annotations.

The readOneProteomDIA function is used to read and filter the data for each individual sample, and it must be available in the environment.

Examples

file <- system.file("extdata", "proteomeDIA_1.xls", package = "SmartPhos")
fileTable <- data.frame(searchType = "proteome", fileName = file,
id = c("sample1", "sample2"))
readProteomeExperimentDIA(fileTable)
#> class: SummarizedExperiment 
#> dim: 2 2 
#> metadata(0):
#> assays(1): Intensity
#> rownames(2): p1 p2
#> rowData names(2): UniprotID Gene
#> colnames(2): sample1 sample2
#> colData names(0):