Read Phosphorylation Experiment Data

readPhosphoExperiment reads and processes phosphorylation experiment data from multiple files, filtering based on localization probability and score difference, and constructs a SummarizedExperiment object.

Usage

readPhosphoExperiment(fileTable, localProbCut = 0.75, scoreDiffCut = 5)

Arguments

fileTable

A data.table or data.frame containing information about the files, including columns for file names, sample names, and other relevant metadata. It must include a column named "searchType" with value "phosphoproteome" for relevant entries.

localProbCut

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

scoreDiffCut

A numeric value specifying the cutoff for score difference. Default is 5.

Value

A SummarizedExperiment object containing the processed phosphorylation data.

Details

This function reads phosphorylation data from multiple files as specified in fileTable, filters the data based on localization probability and score difference, and removes reverse and potential contaminant entries. It constructs an intensity matrix and annotation data, which are then used to create a SummarizedExperiment object.

Examples

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
readPhosphoExperiment(fileTable, localProbCut = 0.75, scoreDiffCut = 5)
#> class: SummarizedExperiment 
#> dim: 2 1 
#> metadata(0):
#> assays(1): Intensity
#> rownames(2): s1 s2
#> rowData names(6): UniprotID Gene ... Sequence site
#> colnames(1): s1
#> colData names(0):