buildSpectraLibPair: Build a spectra library by integrating a pair of spectrum...

In SwathXtend: SWATH extended library generation and statistical data analysis

Description

Build a spectra library by integrating a pair of spectrum libraries

Usage

buildSpectraLibPair(baseLib, extLib, hydroIndex, method = c("time", "hydro",
  "hydrosequence"), includeLength = FALSE, labelBase = NA, labelAddon = NA,
  formatBase = c("peakview", "openswath"), formatExt = c("peakview",
  "openswath"), outputFormat = c("peakview", "openswath"),
  outputFile = "extendedLibrary.txt", plot = FALSE,
  clean = TRUE, merge = TRUE, ...)

Arguments

baseLib	a base library data frame or file
extLib	an external/addon library data frame or file
hydroIndex	a data frame or file containing peptide hydrophobicity index
method	a character string to specify the RT alignment method. One of "time" (default), "hydro" and "hydrosequence" can be selected.
includeLength	a logic value representing if include peptide length as a feature for predicting retention time. Only applicable when method is "hydro".
labelBase	a character string to specify the labels of proteins from the base library
labelAddon	a character string to specify the labels of proteins from the addon library
formatBase	a character string denoting the file format of base library file. One of "peakview" (default) and "opensswath"
formatExt	a character string denoting the file format of addon library file. One of "peakview" (default) and "opensswath"
outputFormat	a character string denoting the file format of the output integrated library. One of "peakview" (default) and "openswath"
outputFile	A character string to specify the sepctra library created
plot	a logic value, representing if plots during processing will be plotted or not
clean	a logic value, representing if the input libraries will be cleaned before integration. Default value is True.
merge	a logic value, representing if the output will be the merged library (default) or the adjusted add-on library.
...	Additional parameters to pass in.

Value

A data frame of the integrated spectrum library

Examples

libfiles <- paste(system.file("files",package="SwathXtend"),
c("Lib2.txt","Lib3.txt"),sep="/")
Lib2_3 <- buildSpectraLibPair(libfiles[1], libfiles[2],  
outputFormat="peakview", clean=TRUE, nomod=TRUE, nomc=TRUE)

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