readLibFile: Load a spectrum library into a data frame

In SwathXtend: SWATH extended library generation and statistical data analysis

Description

Load a spectrum library into a data frame

Usage

readLibFile(file, format = c("peakview", "openswath"), type = c("spectrum",
  "hydro"), clean = TRUE, ...)

Arguments

file	A file of a spectrum library, in .txt or .csv format, can be .gz files.
format	A character string denoting the file format. One of "peakview" (default) and "openswath". If the file format is "peakview", it requires the following columns: Q1: Q1 m/z (precursor m/z); Q3: Q3 m/z (fragment m/z); RT_detected: retention time; protein_name: protein name; isotype: isotype type; relative_intensity: fragment ion intensity; stripped_sequence: peptide sequences without modifications; modification_sequence: peptide sequences with modifications; prec_z: peptide charge; frg_type: fragment type; frg_z: fragment charge; frg_nr: ion number; iRT: calibrated retention time; uniprot_id: database accession number; decoy: whether the peptide a decoy or not; confidence: the confidence of the identified peptide; shared: whether the peptide is shared by multiple proteins; N: a ranking number for the protein. Optional columns for PeakView format libaries include: score: score for peptide identification; prec_y: the precursor ion intensity; rank: ion intensity ranking; mods: modification; nterm: N terminal modification; cterm: C terminal modification; If the file format is "openswath", it must contain the following columns: PrecursorMz: precursor m/z; ProductMz: fragment m/z; Tr_recalibrated: retention time; ProteinName: protein name; GroupLabel: isotype type; LibraryIntensity: fragment ion intensity; PeptideSequence: peptide sequences without modifications; FullUniModPeptideName: peptide sequences with modifications; UniprotID: database accession number; decoy: whether the peptide a decoy or not PrecursorCharge: precursor charge; FragmentType: fragment type (b or y ion); FragmentCharge: fragment charge; FragmentSeriesNumber: fragment ion number.
type	A character string denoting the file type. One of "spectrum" (default) and "hydro"
clean	A logic value, representing if the library will be cleaned.
...	Additional parameters to pass in

Value

a data frame of the library with cleaning process

Examples

file <- paste(system.file("files",package="SwathXtend"),"Lib1.txt",sep="/")
dat <- readLibFile(file)

SwathXtend documentation built on Nov. 8, 2020, 6:42 p.m.