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readPhosphoExperimentDIA reads and processes phosphorylation data from DIA experiments, applying filters for localization probability, and optionally including only reviewed proteins. It constructs a SummarizedExperiment object.

Usage

readPhosphoExperimentDIA(
  fileTable,
  localProbCut = 0.75,
  onlyReviewed = TRUE,
  showProgressBar = FALSE
)

Arguments

fileTable

A data.table or data.frame containing metadata about the files to read. Must include columns fileName, searchType, and optionally outputID.

localProbCut

A numeric value specifying the cutoff for localization probability. Default is 0.75.

onlyReviewed

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

showProgressBar

A logical value indicating whether to show a progress bar. Default is FALSE.

Value

A SummarizedExperiment object containing the processed phosphorylation data.

Details

This function processes phosphorylation data from DIA experiments by filtering based on localization probability and non-zero intensity, handling multiplicity, and optionally including only reviewed proteins. The resulting data is returned as a SummarizedExperiment object with annotations and an intensity matrix.

Examples

file <- system.file("extdata", "phosDIA_1.xls", package = "SmartPhos")
fileTable <- data.frame(searchType = "phosphoproteome", fileName = file,
id = c("Sample_1"))
readPhosphoExperimentDIA(fileTable, localProbCut = 0.75,
onlyReviewed = FALSE, showProgressBar = FALSE)
#> class: SummarizedExperiment 
#> dim: 2 1 
#> metadata(0):
#> assays(1): Intensity
#> rownames(2): s1 s2
#> rowData names(7): UniprotID Gene ... Sequence site
#> colnames(1): Sample_1
#> colData names(0):