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
ordata.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 isTRUE
.- showProgressBar
A
logical
value indicating whether to show a progress bar. Default isFALSE
.
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):