importDIAData: Import data independent acquisition files

In statOmics/MSqRob: Robust statistical inference for quantitative LC-MS proteomics

Import data independent acquisition files

Description

This function generates a peptide data frame from output files originating from either DIAumpire, OpenSWATH, PeakView, Skyline or Spectronaut. It is largely based on the FSWE.generateReports function from the LFQbench package and heavily depends on this package. It is also possible to define a new software format using the FSWE.addSoftwareConfiguration function from the LFQbench package (Navarro et al., 2016).

Usage

importDIAData(experimentFile, aggr_by = "sequence.var",
  softwareSource = "guess", remove_decoys = FALSE)

Arguments

experimentFile	The name of a file. For more details about how this argument can be specified, see read.table.
aggr_by	A character indicating the column by which the data should be aggregated. The default "sequence.var" will aggregate the data over different charge states and modification statuses. If you only want to aggregate over charge states, set aggr_by to "sequence.mod.var". If no aggregation at all is desired, set aggr_by to "none". Data will never be aggregated over different filename.var.
softwareSource	The default, "guess", tries to guess from which software the file originates.
remove_decoys	Should decoys be removed? Defaults to FALSE as removing of decoys is typically done during our preprocessing step. Can be set to TRUE to remove decoys already upfront.

References

Navarro P., Kuharev J., Gillet, L. C., Bernhardt, O. M., MacLean, B., R\"ost, H. L., Tate, S. A., Tsou, C., Reiter, L., Distler, U., Rosenberger, G., Perez-Riverol, Y., Nesvizhskii, A. I., Aebersold, R., and Tenzer, S. (2016) A multicenter study benchmarks software tools for label-free proteome quantification. Nature Biotechnology.

statOmics/MSqRob documentation built on Dec. 8, 2022, 6 a.m.