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Last data update: 2014.03.03

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

buildSpectraLibPair

R Documentation

Build a spectra library by integrating a pair of spectrum libraries

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, parseAcc = TRUE, consolidateAccession = 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 "opensswath"
`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.
`parseAcc`	a logic value, repesenting if the protein accessions will be parsed for consolidation.
`consolidateAccession`	a logic value, representing if the protein accessions will be consolidated to the base libary in the integrated library. Default value is True.
`...`	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)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(SwathXtend)
Loading required package: e1071
Loading required package: openxlsx
Loading required package: VennDiagram
Loading required package: grid
Loading required package: futile.logger
Loading required package: lattice
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/SwathXtend/buildSpectraLibPair.Rd_%03d_medium.png", width=480, height=480)
> ### Name: buildSpectraLibPair
> ### Title: Build a spectra library by integrating a pair of spectrum
> ###   libraries
> ### Aliases: buildSpectraLibPair
> 
> ### ** 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)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>