R/WSInterface.R
In Yaroslav-Lyutvinskiy/MZAccessR: R Interface to mzAccess Web-API
# *******************************************************************************
# Copyright 2015-2017 Yaroslav Lyutvinskiy <Yaroslav.Lyutvinskiy@ki.se> and
# Roland Nilsson <Roland.Nilsson@ki.se>
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.using System;
#
# *******************************************************************************
setClass( 'ArrayOfArrayOfDouble' ,
representation(
.Data = 'list') ,
contains = c( 'list' ) )
setAs('XMLInternalElementNode', 'ArrayOfArrayOfDouble',
function (from, to = "ArrayOfArrayOfDouble", strict = TRUE)
xmlSApply(from, as, "ArrayOfDouble")
)
setClass( 'ArrayOfDouble' ,
representation(
.Data = 'numeric') ,
contains = c( 'numeric' ) )
setAs('XMLInternalElementNode', 'ArrayOfDouble',
function (from, to = "ArrayOfDouble", strict = TRUE)
xmlSApply(from, as, "numeric")
)
setAs('character', 'ArrayOfDouble',
function (from, to = "ArrayOfDouble", strict = TRUE)
new("ArrayOfDouble", as(from, "character"))
)
setAs('integer', 'ArrayOfDouble',
function (from, to = "ArrayOfDouble", strict = TRUE)
new("ArrayOfDouble", as(from, "integer"))
)
setAs('logical', 'ArrayOfDouble',
function (from, to = "ArrayOfDouble", strict = TRUE)
new("ArrayOfDouble", as(from, "logical"))
)
setClass( 'ArrayOfFragmentationInfo' ,
representation(
.Data = 'list') ,
contains = c( 'list' ) )
setAs('XMLInternalElementNode', 'ArrayOfFragmentationInfo',
function (from, to = "ArrayOfFragmentationInfo", strict = TRUE)
xmlSApply(from, as, "FragmentationInfo")
)
setClass( 'ArrayOfString' ,
representation(
.Data = 'character') ,
contains = c( 'character' ) )
setAs('XMLInternalElementNode', 'ArrayOfString',
function (from, to = "ArrayOfString", strict = TRUE)
xmlSApply(from, as, "character")
)
setAs('integer', 'ArrayOfString',
function (from, to = "ArrayOfString", strict = TRUE)
new("ArrayOfString", as(from, "integer"))
)
setAs('numeric', 'ArrayOfString',
function (from, to = "ArrayOfString", strict = TRUE)
new("ArrayOfString", as(from, "numeric"))
)
setAs('logical', 'ArrayOfString',
function (from, to = "ArrayOfString", strict = TRUE)
new("ArrayOfString", as(from, "logical"))
)
setClass( 'FileListResult.ErrorMessage' ,
representation(
FileListResult = 'ArrayOfString',
ErrorMessage = 'character') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'FileListResult.ErrorMessage',
function (from, to = "FileListResult.ErrorMessage", strict = TRUE)
coerceListToS4(from, new("FileListResult.ErrorMessage"))
)
setClass( 'FileName.Cache' ,
representation(
FileName = 'character',
Cache = 'logical') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'FileName.Cache',
function (from, to = "FileName.Cache", strict = TRUE)
coerceListToS4(from, new("FileName.Cache"))
)
setClass( 'FileName.MZLow.MZHigh.RT.Cache.Profile' ,
representation(
FileName = 'character',
MZLow = 'numeric',
MZHigh = 'numeric',
RT = 'numeric',
Cache = 'logical',
Profile = 'logical') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'FileName.MZLow.MZHigh.RT.Cache.Profile',
function (from, to = "FileName.MZLow.MZHigh.RT.Cache.Profile",
strict = TRUE)
coerceListToS4(from, new("FileName.MZLow.MZHigh.RT.Cache.Profile"))
)
setClass( 'FileName.MZLow.MZHigh.RTLow.RTHigh' ,
representation(
FileName = 'character',
MZLow = 'numeric',
MZHigh = 'numeric',
RTLow = 'numeric',
RTHigh = 'numeric') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'FileName.MZLow.MZHigh.RTLow.RTHigh',
function (from, to = "FileName.MZLow.MZHigh.RTLow.RTHigh", strict = TRUE)
coerceListToS4(from, new("FileName.MZLow.MZHigh.RTLow.RTHigh"))
)
setClass( 'FileName.MZLow.MZHigh.RTLow.RTHigh.Cache' ,
representation(
FileName = 'character',
MZLow = 'numeric',
MZHigh = 'numeric',
RTLow = 'numeric',
RTHigh = 'numeric',
Cache = 'logical') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'FileName.MZLow.MZHigh.RTLow.RTHigh.Cache',
function (from, to = "FileName.MZLow.MZHigh.RTLow.RTHigh.Cache",
strict = TRUE)
coerceListToS4(from, new("FileName.MZLow.MZHigh.RTLow.RTHigh.Cache"))
)
setClass( 'FileName.MZLow.MZHigh.RTLow.RTHigh.Cache.Profile' ,
representation(
FileName = 'character',
MZLow = 'numeric',
MZHigh = 'numeric',
RTLow = 'numeric',
RTHigh = 'numeric',
Cache = 'logical',
Profile = 'logical') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'FileName.MZLow.MZHigh.RTLow.RTHigh.Cache.Profile',
function (from, to = "FileName.MZLow.MZHigh.RTLow.RTHigh.Cache.Profile",
strict = TRUE)
coerceListToS4(from, new("FileName.MZLow.MZHigh.RTLow.RTHigh.Cache.Profile"))
)
setClass( 'FileName.MZLow.MZHigh.RTLow.RTHigh.Profile' ,
representation(
FileName = 'character',
MZLow = 'numeric',
MZHigh = 'numeric',
RTLow = 'numeric',
RTHigh = 'numeric',
Profile = 'logical') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'FileName.MZLow.MZHigh.RTLow.RTHigh.Profile',
function (from, to = "FileName.MZLow.MZHigh.RTLow.RTHigh.Profile",
strict = TRUE)
coerceListToS4(from, new("FileName.MZLow.MZHigh.RTLow.RTHigh.Profile"))
)
setClass( 'FileName.MZLow.MZHigh.ScanNumber.Cache.Profile' ,
representation(
FileName = 'character',
MZLow = 'numeric',
MZHigh = 'numeric',
ScanNumber = 'integer',
Cache = 'logical',
Profile = 'logical') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'FileName.MZLow.MZHigh.ScanNumber.Cache.Profile',
function (from, to = "FileName.MZLow.MZHigh.ScanNumber.Cache.Profile",
strict = TRUE)
coerceListToS4(from, new("FileName.MZLow.MZHigh.ScanNumber.Cache.Profile"))
)
setClass( 'FileName.RT.Cache' ,
representation(
FileName = 'character',
RT = 'numeric',
Cache = 'logical') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'FileName.RT.Cache',
function (from, to = "FileName.RT.Cache", strict = TRUE)
coerceListToS4(from, new("FileName.RT.Cache"))
)
setClass( 'FileName.ScanNumber.Cache' ,
representation(
FileName = 'character',
ScanNumber = 'integer',
Cache = 'logical') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'FileName.ScanNumber.Cache',
function (from, to = "FileName.ScanNumber.Cache", strict = TRUE)
coerceListToS4(from, new("FileName.ScanNumber.Cache"))
)
setClass( 'FileNames.MZLow.MZHigh.RTLow.RTHigh.Cache' ,
representation(
FileNames = 'ArrayOfString',
MZLow = 'ArrayOfDouble',
MZHigh = 'ArrayOfDouble',
RTLow = 'ArrayOfDouble',
RTHigh = 'ArrayOfDouble',
Cache = 'logical') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'FileNames.MZLow.MZHigh.RTLow.RTHigh.Cache',
function (from, to = "FileNames.MZLow.MZHigh.RTLow.RTHigh.Cache", strict = TRUE)
coerceListToS4(from, new("FileNames.MZLow.MZHigh.RTLow.RTHigh.Cache"))
)
setClass( 'FileNames.MZLow.MZHigh.RTLow.RTHigh.Cache.Profile' ,
representation(
FileNames = 'ArrayOfString',
MZLow = 'ArrayOfDouble',
MZHigh = 'ArrayOfDouble',
RTLow = 'ArrayOfDouble',
RTHigh = 'ArrayOfDouble',
Cache = 'logical',
Profile = 'logical') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'FileNames.MZLow.MZHigh.RTLow.RTHigh.Cache.Profile',
function (from, to = "FileNames.MZLow.MZHigh.RTLow.RTHigh.Cache.Profile", strict = TRUE)
coerceListToS4(from, new("FileNames.MZLow.MZHigh.RTLow.RTHigh.Cache.Profile"))
)
setClass( 'FileNames.MZLow.MZHigh.RTLow.RTHigh.Profile' ,
representation(
FileNames = 'ArrayOfString',
MZLow = 'ArrayOfDouble',
MZHigh = 'ArrayOfDouble',
RTLow = 'ArrayOfDouble',
RTHigh = 'ArrayOfDouble',
Profile = 'logical') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'FileNames.MZLow.MZHigh.RTLow.RTHigh.Profile',
function (from, to = "FileNames.MZLow.MZHigh.RTLow.RTHigh.Profile", strict = TRUE)
coerceListToS4(from, new("FileNames.MZLow.MZHigh.RTLow.RTHigh.Profile"))
)
setClass( 'FragmentationInfo' ,
representation(
RT = 'numeric',
ParentMZ = 'numeric',
ScanNumber = 'integer',
MSOrder = 'integer',
Description = 'character') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'FragmentationInfo',
function (from, to = "FragmentationInfo", strict = TRUE)
coerceListToS4(from, new("FragmentationInfo"))
)
setClass( 'GetAreaArrayResult.ErrorMessage' ,
representation(
GetAreaArrayResult = 'ArrayOfArrayOfDouble',
ErrorMessage = 'character') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'GetAreaArrayResult.ErrorMessage',
function (from, to = "GetAreaArrayResult.ErrorMessage", strict = TRUE)
coerceListToS4(from, new("GetAreaArrayResult.ErrorMessage"))
)
setClass( 'GetAreaResult.ErrorMessage' ,
representation(
GetAreaResult = 'ArrayOfDouble',
ErrorMessage = 'character') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'GetAreaResult.ErrorMessage',
function (from, to = "GetAreaResult.ErrorMessage", strict = TRUE)
coerceListToS4(from, new("GetAreaResult.ErrorMessage"))
)
setClass( 'GetAverageSpectrumResult.ErrorMessage' ,
representation(
GetAverageSpectrumResult = 'ArrayOfDouble',
ErrorMessage = 'character') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'GetAverageSpectrumResult.ErrorMessage',
function (from, to = "GetAverageSpectrumResult.ErrorMessage", strict = TRUE)
coerceListToS4(from, new("GetAverageSpectrumResult.ErrorMessage"))
)
setClass( 'GetChromatogramArrayResult.ErrorMessage' ,
representation(
GetChromatogramArrayResult = 'ArrayOfArrayOfDouble',
ErrorMessage = 'character') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'GetChromatogramArrayResult.ErrorMessage',
function (from, to = "GetChromatogramArrayResult.ErrorMessage", strict = TRUE)
coerceListToS4(from, new("GetChromatogramArrayResult.ErrorMessage"))
)
setClass( 'GetChromatogramResult.ErrorMessage' ,
representation(
GetChromatogramResult = 'ArrayOfDouble',
ErrorMessage = 'character') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'GetChromatogramResult.ErrorMessage',
function (from, to = "GetChromatogramResult.ErrorMessage", strict = TRUE)
coerceListToS4(from, new("GetChromatogramResult.ErrorMessage"))
)
setClass( 'GetFragmentationEventsResult.ErrorMessage' ,
representation(
GetFragmentationEventsResult = 'ArrayOfFragmentationInfo',
ErrorMessage = 'character') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'GetFragmentationEventsResult.ErrorMessage',
function (from, to = "GetFragmentationEventsResult.ErrorMessage", strict = TRUE)
coerceListToS4(from, new("GetFragmentationEventsResult.ErrorMessage"))
)
setClass( 'GetMZRangeResult.ErrorMessage' ,
representation(
GetMZRangeResult = 'ArrayOfDouble',
ErrorMessage = 'character') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'GetMZRangeResult.ErrorMessage',
function (from, to = "GetMZRangeResult.ErrorMessage", strict = TRUE)
coerceListToS4(from, new("GetMZRangeResult.ErrorMessage"))
)
setClass( 'GetRTFromScanNumberResult.ErrorMessage' ,
representation(
GetRTFromScanNumberResult = 'numeric',
ErrorMessage = 'character') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'GetRTFromScanNumberResult.ErrorMessage',
function (from, to = "GetRTFromScanNumberResult.ErrorMessage",
strict = TRUE)
coerceListToS4(from, new("GetRTFromScanNumberResult.ErrorMessage"))
)
setClass( 'GetRTRangeResult.ErrorMessage' ,
representation(
GetRTRangeResult = 'ArrayOfDouble',
ErrorMessage = 'character') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'GetRTRangeResult.ErrorMessage',
function (from, to = "GetRTRangeResult.ErrorMessage", strict = TRUE)
coerceListToS4(from, new("GetRTRangeResult.ErrorMessage"))
)
setClass( 'GetScanNumberFromRTResult.ErrorMessage' ,
representation(
GetScanNumberFromRTResult = 'integer',
ErrorMessage = 'character') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'GetScanNumberFromRTResult.ErrorMessage',
function (from, to = "GetScanNumberFromRTResult.ErrorMessage",
strict = TRUE)
coerceListToS4(from, new("GetScanNumberFromRTResult.ErrorMessage"))
)
setClass( 'GetSpectraArrayResult.ErrorMessage' ,
representation(
GetSpectraArrayResult = 'ArrayOfArrayOfDouble',
ErrorMessage = 'character') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'GetSpectraArrayResult.ErrorMessage',
function (from, to = "GetSpectraArrayResult.ErrorMessage", strict = TRUE)
coerceListToS4(from, new("GetSpectraArrayResult.ErrorMessage"))
)
setClass( 'GetSpectrumbyRTResult.ErrorMessage' ,
representation(
GetSpectrumbyRTResult = 'ArrayOfDouble',
ErrorMessage = 'character') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'GetSpectrumbyRTResult.ErrorMessage',
function (from, to = "GetSpectrumbyRTResult.ErrorMessage", strict = TRUE)
coerceListToS4(from, new("GetSpectrumbyRTResult.ErrorMessage"))
)
setClass( 'GetSpectrumbyScanNumberResult.ErrorMessage' ,
representation(
GetSpectrumbyScanNumberResult = 'ArrayOfDouble',
ErrorMessage = 'character') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'GetSpectrumbyScanNumberResult.ErrorMessage',
function (from, to = "GetSpectrumbyScanNumberResult.ErrorMessage",
strict = TRUE)
coerceListToS4(from, new("GetSpectrumbyScanNumberResult.ErrorMessage"))
)
setClass( 'GetTotalArrayResult.ErrorMessage' ,
representation(
GetTotalArrayResult = 'ArrayOfDouble',
ErrorMessage = 'character') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'GetTotalArrayResult.ErrorMessage',
function (from, to = "GetTotalArrayResult.ErrorMessage", strict = TRUE)
coerceListToS4(from, new("GetTotalArrayResult.ErrorMessage"))
)
setClass( 'GetTotalResult.ErrorMessage' ,
representation(
GetTotalResult = 'numeric',
ErrorMessage = 'character') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'GetTotalResult.ErrorMessage',
function (from, to = "GetTotalResult.ErrorMessage", strict = TRUE)
coerceListToS4(from, new("GetTotalResult.ErrorMessage")))
setMethod("toSOAP", c("logical", "XMLInternalElementNode", type = "PrimitiveSOAPType"),
function(obj, con = xmlOutputBuffer(header=""), type = NULL, literal = FALSE, elementFormQualified = FALSE, ...)
{
if (literal){
if (.Primitive("as.logical")(obj)) {
newXMLTextNode("true",parent=con)
}
else {
newXMLTextNode("false",parent = con)
}
}else{
if (.Primitive("as.logical")(obj))
"true"
else
"false"
}
})
setAs('list', 'ArrayOfDouble',
function (from, to = "ArrayOfDouble", strict = TRUE)
new("ArrayOfDouble", as(from, "list")))
setAs('list', 'ArrayOfString',
function (from, to = "ArrayOfString", strict = TRUE)
new("ArrayOfString", as(from, "list")))
setAs('matrix', 'ArrayOfArrayOfDouble',
function (from, to = "ArrayOfArrayOfDouble", strict = TRUE){
Res = new("ArrayOfArrayOfDouble")
for(i in 1:dim(from)[2]){
Res[[i]]=from[,i]
}
Res
})
#' @export
MZRange <- setClass("MZRange", slots = c(MinMZ="numeric", MaxMZ="numeric"))
#' @export
RTRange <- setClass("RTRange", slots = c(MinRT="numeric", MaxRT="numeric"))
#' @export
LCMSArea <- setClass("LCMSArea", slots = c(RTRange="RTRange", MZRange="MZRange"))
WDSLEnvir = new.env()
#' Setup for Web-server
#'
#' Checks server connection and loads function prototypes.
#' All other functions become working only afrter SetupServer call.
#'
#' @param ServerURL - WDSL page of mzAccess web server
#' @return None
#' @examples
#' SetupServer()
#' @export
SetupServer =
function(ServerURL = "http://charon.ad.cmm.se:6060/MzAccessPublicTest/Service.asmx?WSDL"){
wsdl = processWSDL(ServerURL)
assign("wsdl", wsdl, envir = WDSLEnvir)
iface= genSOAPClientInterface(wsdl)
assign("iface", iface, envir = WDSLEnvir)
}
#' Get XIC Chromatogram
#'
#' Gets eXtracted Ion Current (XIC) chromatograms for specified LC-MS area.
#' Corresponds to mzAccess web-service API function GetChromatogram
#'
#' @param FileName - Name of original raw mass spectrometry file. Can be stated with or without path and extention
#' @param MZLow - Minimum m/z value for LC-MS area requested
#' @param MZHigh - Maximum m/z value for LC-MS area requested
#' @param RTLow - Minimum retention time value for LC-MS area requested
#' @param RTHigh - Maximum retention time value for LC-MS area requested
#' @param Cache - If TRUE data will be loaded from fast access cache, if FALSE - from original raw files
#' @return Data frame of Retention Time and Intensities for requested LC-MS area
#' @examples
#' GetChromatogram("Thermo_QE_cells_72h_LA_3",148.0584342,148.0624342,0,16)
#' @export
#' @import XML
#' @import XMLSchema
#' @import SSOAP
GetChromatogram =
function(FileName, MZLow, MZHigh, RTLow, RTHigh, Cache=TRUE){
iface = get("iface", envir = WDSLEnvir)
CH1=iface@functions$GetChromatogram(list(
FileName=FileName,
MZLow=MZLow, MZHigh = MZHigh,
RTLow = RTLow, RTHigh = RTHigh ,
Cache=Cache))
if (is.character(CH1@ErrorMessage)) print(CH1@ErrorMessage)
L=CH1@GetChromatogramResult
CHR=data.frame(RT=L[c(TRUE,FALSE)],Intensity=L[c(FALSE,TRUE)])
return(CHR)
}
#' Get LC-MS Area signals
#'
#' Gets all non-zero signals for specified LC-MS area.
#' Corresponds to mzAccess web-service API function GetArea
#'
#' @param FileName - Name of original raw mass spectrometry file. Can be stated with or without path and extention
#' @param MZLow - Minimum m/z value for LC-MS area requested
#' @param MZHigh - Maximum m/z value for LC-MS area requested
#' @param RTLow - Minimum retention time value for LC-MS area requested
#' @param RTHigh - Maximum retention time value for LC-MS area requested
#' @param Cache - If TRUE data will be loaded from fast access cache, if FALSE - from original raw files
#' @param Profile - If TRUE data will presented in profile mode how is was acquired by mass spectrometer, If FALSE data will be presented in peak centroided mode
#' @return Data frame of Mass, Retention Time and Intensities for requested LC-MS area
#' @examples
#' GetArea(FileName="Thermo_QE_cells_72h_UL_1",149.047,149.074, RTLow = 8.2, RTHigh = 8.5,Profile = TRUE, Cache = FALSE)
#' @export
GetArea =
function(FileName, MZLow, MZHigh, RTLow, RTHigh, Cache=TRUE, Profile = FALSE){
iface = get("iface", envir = WDSLEnvir)
Ar=iface@functions$GetArea(list(
FileName=FileName,
MZLow=MZLow, MZHigh = MZHigh,
RTLow = RTLow, RTHigh = RTHigh ,
Cache=Cache, Profile = Profile))
if (is.character(Ar@ErrorMessage)) print(Ar@ErrorMessage)
L=Ar@GetAreaResult
AREA=data.frame(Mass=L[c(TRUE,FALSE,FALSE)],RT=L[c(FALSE,TRUE,FALSE)],Intensity=L[c(FALSE,FALSE,TRUE)])
return(AREA)
}
#' Get averaged spectrum
#'
#' Get spectrum averaged (or summed) within RT interval
#' Corresponds to mzAccess web-service API function GetAverageSpectrum
#' Averaging algorithm is vendor specific, therefore function has no cache option
#'
#' @param FileName - Name of original raw mass spectrometry file. Can be stated with or without path and extention
#' @param MZLow - Minimum m/z value to be included in spectrum
#' @param MZHigh - Maximum m/z value to be included in spectrum
#' @param RTLow - Minimum retention time value for RT range of averaged spectrum
#' @param RTHigh - Maximum retention time value for RT range of averaged spectrum
#' @param Profile - If TRUE data will presented in profile mode how is was acquired by mass spectrometer, If FALSE data will be presented in peak centroided mode
#' @return Data frame of Mass and Intensities for requested LC-MS area
#' @examples
#' GetAvgSpectrum("Thermo_QE_cells_72h_LA_3", MZLow = 50, MZHigh = 400, RTLow = 6, RTHigh = 8, Profile = FALSE)
#' @export
GetAvgSpectrum =
function(FileName, MZLow, MZHigh, RTLow, RTHigh, Profile = FALSE){
iface = get("iface", envir = WDSLEnvir)
Sp=iface@functions$GetAverageSpectrum(list(
FileName=FileName,
MZLow=MZLow, MZHigh = MZHigh,
RTLow = RTLow, RTHigh = RTHigh ,
Profile = Profile))
if (is.character(Sp@ErrorMessage)) print(Sp@ErrorMessage)
L=Sp@GetAverageSpectrumResult
SPC=data.frame(Mass=L[c(TRUE,FALSE)],Intensity=L[c(FALSE,TRUE)])
return(SPC)
}
#' Get spectrum for RT
#'
#' Get Single scan spectrum on certain RT.
#' Web-service will provide first spectrum where RT is not less than specified
#' Corresponds to mzAccess web-service API function GetSpectrumbyRT
#'
#' @param FileName - Name of original raw mass spectrometry file. Can be stated with or without path and extention
#' @param MZLow - Minimum m/z value to be included in spectrum
#' @param MZHigh - Maximum m/z value to be included in spectrum
#' @param RT - retention time for which spectrum will be searched.
#' @param Cache - If TRUE data will be loaded from fast access cache, if FALSE - from original raw files
#' @param Profile - If TRUE data will presented in profile mode how is was acquired by mass spectrometer, If FALSE data will be presented in peak centroided mode
#' @return Data frame of Mass and Intensities for requested LC-MS area
#' @examples
#' GetSpectrumByRT("Thermo_QE_cells_72h_LA_3", MZLow = 50, MZHigh = 400, RT = 6, Cache = FALSE, Profile = FALSE)
#' @export
GetSpectrumByRT =
function(FileName, MZLow, MZHigh, RT, Cache=FALSE, Profile = FALSE){
iface = get("iface", envir = WDSLEnvir)
Sp=iface@functions$GetSpectrumByRT(list(
FileName=FileName,
MZLow=MZLow, MZHigh = MZHigh,
RT = RT,
Cache=Cache, Profile = Profile))
if (is.character(Sp@ErrorMessage)) print(Sp@ErrorMessage)
L=Sp@GetSpectrumByRTResult
SPC=data.frame(Mass=L[c(TRUE,FALSE)],Intensity=L[c(FALSE,TRUE)])
return(SPC)
}
#' Get spectrum for scan number
#'
#' Get Single scan spectrum for certain scan.
#' Corresponds to mzAccess web-service API function GetSpectrumbyScanNumber
#'
#' @param FileName - Name of original raw mass spectrometry file. Can be stated with or without path and extention
#' @param MZLow - Minimum m/z value to be included in spectrum
#' @param MZHigh - Maximum m/z value to be included in spectrum
#' @param ScanNumber - scan number for requested spectrum.
#' @param Profile - If TRUE data will presented in profile mode how is was acquired by mass spectrometer, If FALSE data will be presented in peak centroided mode
#' @param Cache - If TRUE data will be loaded from fast access cache, if FALSE - from original raw files
#' @return Data frame of Mass and Intensities for requested LC-MS area
#' @examples
#' GetSpectrumByScanNumber("Thermo_QE_cells_72h_LA_3", MZLow = 50, MZHigh = 400, ScanNumber = 1000, Profile = TRUE)
#' @export
GetSpectrumByScanNumber =
function(FileName, MZLow, MZHigh, ScanNumber, Cache=FALSE, Profile = FALSE){
iface = get("iface", envir = WDSLEnvir)
Sp=iface@functions$GetSpectrumByScanNumber(list(
FileName=FileName,
MZLow=MZLow, MZHigh = MZHigh,
ScanNumber = ScanNumber,
Cache=Cache, Profile = Profile))
if (is.character(Sp@ErrorMessage)) print(Sp@ErrorMessage)
L=Sp@GetSpectrumByScanNumberResult
SPC=data.frame(Mass=L[c(TRUE,FALSE)],Intensity=L[c(FALSE,TRUE)])
return(SPC)
}
#' Get scan number for retention time
#'
#' Get scan number
#' Corresponds to mzAccess web-service API function GetScanNumberFromRT
#' Web-service will provide first scan number where RT is not less than specified
#'
#' @param FileName - Name of original raw mass spectrometry file. Can be stated with or without path and extention
#' @param RT - retention time for which spectrum will be searched.
#' @param Cache - If TRUE scan number will be loaded from fast access cache, if FALSE - from original raw files
#' @return Interger scan number
#' @examples
#' GetScanNumberFromRT("Thermo_QE_cells_72h_LA_3",6)
#' @export
GetScanNumberFromRT =
function(FileName, RT, Cache=FALSE){
iface = get("iface", envir = WDSLEnvir)
Scan=iface@functions$GetScanNumberFromRT(list(
FileName=FileName,
RT = RT, Cache=Cache))
if (is.character(Scan@ErrorMessage)) print(Scan@ErrorMessage)
L=Scan@GetScanNumberFromRTResult
return(L)
}
#' Get retention time for scan number
#'
#' Get retention time for scan number
#' Corresponds to mzAccess web-service API function GetRTFromScanNumber
#' Web-service will provide first scan number where RT is not less than specified
#'
#' @param FileName - Name of original raw mass spectrometry file. Can be stated with or without path and extention
#' @param RT - retention time for which spectrum will be searched.
#' @param Cache - If TRUE retention time value (in minutes) will be loaded from fast access cache, if FALSE - from original raw files
#' @return Retention time value
#' @examples
#' GetRTFromScanNumber("Thermo_QE_cells_72h_LA_3",1000)
#' @export
GetRTFromScanNumber =
function(FileName, ScanNumber, Cache=FALSE){
iface = get("iface", envir = WDSLEnvir)
RT=iface@functions$GetRTFromScanNumber(list(
FileName=FileName,
ScanNumber = ScanNumber, Cache=Cache))
if (is.character(RT@ErrorMessage)) print(RT@ErrorMessage)
L=RT@GetRTFromScanNumberResult
return(L)
}
#' Get mass range for spectra in file
#'
#' Get mass range for spectra in file
#' Corresponds to mzAccess web-service API function GetMZRange
#'
#' @param FileName - Name of original raw mass spectrometry file. Can be stated with or without path and extention
#' @param Cache - If TRUE Mass Range will show minimum amd maximim masses avialable in spectra through the file, if FALSE - it will return Mass Interval where masses were scanned by mass spectrometer
#' @return MassRange object with slots MinMZ,MaxMZ
#' @examples
#' GetMZRange("Thermo_QE_cells_72h_LA_3")
#' @export
GetMZRange =
function(FileName, Cache=FALSE){
iface = get("iface", envir = WDSLEnvir)
Range=iface@functions$GetMZRange(
list(FileName=FileName, Cache=Cache))
if (is.character(Range@ErrorMessage)) print(Range@ErrorMessage)
R=MZRange(MinMZ=Range@GetMZRangeResult[1],
MaxMZ=Range@GetMZRangeResult[2])
return(R)
}
#' Get retention time range for spectra in file
#'
#' Get retention time range for spectra in file
#' Corresponds to mzAccess web-service API function GetRTRange
#'
#' @param FileName - Name of original raw mass spectrometry file. Can be stated with or without path and extention
#' @param Cache - If TRUE RT Range will show RTs for first and last spectra in spectra through the file, if FALSE - it will retention time range as registered by mass spectrometer
#' @return RTRange object with slots MinRT,MaxRT
#' @examples
#' GetRTRange("Thermo_QE_cells_72h_LA_3")
#' @export
GetRTRange =
function(FileName, Cache=FALSE){
iface = get("iface", envir = WDSLEnvir)
Range=iface@functions$GetRTRange(
list(FileName=FileName, Cache=Cache))
if (is.character(Range@ErrorMessage)) print(Range@ErrorMessage)
R=RTRange(MinRT=Range@GetRTRangeResult[1],
MaxRT=Range@GetRTRangeResult[2])
return(R)
}
#' Get list of avialable files
#'
#' Get list of avialable files by provided mask
#' Corresponds to mzAccess web-service API function FileList
#'
#' @param FileMask - File mask for file search Applied to file name only without extension. Case insensitive. Can contain "*"and "?" mask symbols
#' @return List of available file names
#' @examples
#' FileList("*72h*")
#' @export
FileList =
function(FileMask = "*"){
iface = get("iface", envir = WDSLEnvir)
FList =iface@functions$FileList(FileMask)
if (is.character(FList@ErrorMessage)) print(FList@ErrorMessage)
L = FList@FileListResult@.Data
return(as.list(L))
}
#' Get data frame of fragmentation events in requested LC-MS area
#'
#' Get data frame of fragmentation events in requested LC-MS area
#' Corresponds to mzAccess web-service API function GetFragmentationEvents
#'
#' @param FileName - Name of original raw mass spectrometry file.
#' @param MZLow - Minimum parent ion m/z value to be included in event list
#' @param MZHigh - Maximum parent ion m/z value to be included in event list
#' @param RTLow - Minimum retention time value to be included in event list
#' @param RTHigh - Maximum retention time value to be included in event list
#' @return Data frame of fragmentation events inside of desired LC-MS region
#' Includes Scan Number (to use with function GetSpectraByScanNumber),
#' Mass of parent ion,
#' Retention time of fragmentation event
#' MSOrder - if 2 - that is MSMS spectra, if more it is high order MSN spectra
#' Desc - description of spectrum
#' @examples
#' GetFragmentationEvents("Agilent_QTOF_plasma_1.d",200,250,6,6.5)
#' @export
GetFragmentationEvents =
function(FileName, MZLow, MZHigh, RTLow, RTHigh){
iface = get("iface", envir = WDSLEnvir)
SPInfo = iface@functions$GetFragmentationEvents(list(
FileName=FileName,
MZLow = MZLow, MZHigh = MZHigh,
RTLow = RTLow, RTHigh = RTHigh))
if (is.character(SPInfo@ErrorMessage)) print(SPInfo@ErrorMessage)
df = data.frame(
ScanNumber=as.numeric(sapply(SPInfo@GetFragmentationEventsResult,function(x)x@ScanNumber,simplify = TRUE )),
ParentMZ=as.numeric(sapply(SPInfo@GetFragmentationEventsResult,function(x)x@ParentMZ,simplify = TRUE )),
RT=as.numeric(sapply(SPInfo@GetFragmentationEventsResult,function(x)x@RT,simplify = TRUE )),
MSOrder=as.numeric(sapply(SPInfo@GetFragmentationEventsResult,function(x)x@MSOrder,simplify = TRUE )),
Description = as.character(sapply(SPInfo@GetFragmentationEventsResult,function(x)x@Description,simplify = TRUE ))
)
return(df)
}
#' Get Array of XIC Chromatogram
#'
#' Batch analog of GetChromatogram function.
#' Gets array of eXtracted Ion Current (XIC) chromatograms for specified LC-MS areas.
#' Equal length of incoming lists is assumed.
#' Corresponds to mzAccess web-service API function GetChromatogramsArray
#'
#' @param FileNames - List of names of original raw mass spectrometry file.
#' @param MZLow - List of minimum m/z values for LC-MS areas requested
#' @param MZHigh - List of maximum m/z values for LC-MS areas requested
#' @param RTLow - List of minimum retention time values for LC-MS areas requested
#' @param RTHigh - List of maximum retention time values for LC-MS areas requested
#' @param Cache - If TRUE data will be loaded from fast access cache, if FALSE - from original raw files
#' @return List of data frames. Each n-th data frame represent single XIC chromatogram specified
#' by n-th members of incoming arrays and consist of
#' of Retention Time and Intensities for requested LC-MS area
#' @examples
#' Coordinates for the glutamate peak observed in Figure 2A in reference paper
#' mz0 <- 148.0604342; dMz <- 0.002; d13C <- 1.0033548378;rtMin <- 8; rtMax <- 9;
#' Get Chromatograms for 1-st and 6-th isotopes
#'chrom <- GetChromatogramArray(
#' rep("Thermo_QE_cells_72h_LA_1", 2),
#' c(mz0-dMz, mz0 + 5*d13C - dMz),
#' c(mz0+dMz, mz0 + 5*d13C + dMz),
#' rep(rtMin, 2), rep(rtMax, 2))
#' @export
GetChromatogramArray =
function(FileNames,MZLows,MZHighs,RTLows,RTHighs,Cache=TRUE){
iface = get("iface", envir = WDSLEnvir)
ArAr=iface@functions$GetChromatogramArray(list(
FileNames=FileNames,
MZLow=MZLows,
MZHigh=MZHighs,
RTLow=RTLows,
RTHigh=RTHighs,
Cache=Cache))
if (is.character(ArAr@ErrorMessage)) print(ArAr@ErrorMessage)
Res=lapply(ArAr@GetChromatogramArrayResult,function(L){
data.frame(
RT=L[c(TRUE,FALSE)],
Intensity=L[c(FALSE,TRUE)])})
return(Res)
}
#' Get Array of LC-MS Area signals
#'
#' Batch analog of GetArea function.
#' Gets List of data frames where each data frame contains all non-zero signals for one of specified LC-MS areas.
#' Equal length of incoming lists is assumed.
#' Corresponds to mzAccess web-service API function GetAreasArray
#'
#' @param FileNames - List of names of original raw mass spectrometry file.
#' @param MZLow - List of minimum m/z values for LC-MS areas requested
#' @param MZHigh - List of maximum m/z values for LC-MS areas requested
#' @param RTLow - List of minimum retention time values for LC-MS areas requested
#' @param RTHigh - List of maximum retention time values for LC-MS areas requested
#' @param Cache - If TRUE data will be loaded from fast access cache, if FALSE - from original raw files
#' @param Profile - If TRUE data will presented in profile mode how is was acquired by mass spectrometer, If FALSE data will be presented in peak centroided mode
#' @return List of data frames. Each n-th data frame contains Mass, Retention Time and Intensities for all non-zero signals for LC-MS area, specified
#' by n-th members of incoming arrays.
#' @examples
#' Coordinates for the glutamate peak observed in Figure 2A in reference paper
#' mz0 <- 148.0604342; dMz <- 0.002; d13C <- 1.0033548378;rtMin <- 8; rtMax <- 9;
#' Get MZ/RT areas for 1-st and 6-th isotopes
#' Areas <- GetAreaArray(
#' rep("Thermo_QE_cells_72h_LA_1", 2),
#' c(mz0-dMz, mz0 + 5*d13C - dMz),
#' c(mz0+dMz, mz0 + 5*d13C + dMz),
#' rep(rtMin, 2), rep(rtMax, 2))
#' @export
GetAreaArray =
function(FileNames,MZLows,MZHighs,RTLows,RTHighs,Cache=TRUE,Profile=FALSE){
iface = get("iface", envir = WDSLEnvir)
ArAr=iface@functions$GetAreaArray(list(
FileNames=FileNames,
MZLow=MZLows,
MZHigh=MZHighs,
RTLow=RTLows,
RTHigh=RTHighs,
Cache=Cache,
Profile=Profile))
if (is.character(ArAr@ErrorMessage)) print(ArAr@ErrorMessage)
Res=lapply(ArAr@GetAreaArrayResult,function(L){
data.frame(
Mass=L[c(TRUE,FALSE,FALSE)],
RT=L[c(FALSE,TRUE,FALSE)],
Intensity=L[c(FALSE,FALSE,TRUE)])})
return(Res)
}
#' Get Array of averaged spectra
#'
#' Batch analog of GetAveSpectrum function.
#' Get Array of spectra averaged (or summed) within desired RT intervals
#' Corresponds to mzAccess web-service API function GetSpectrumArray
#' Equal length of incoming lists is assumed.
#' Averaging algorithm is vendor specific, therefore function has no cache option
#'
#' @param FileName - Name of original raw mass spectrometry file. Can be stated with or without path and extention
#' @param MZLow - List of minimum m/z values to be included in spectrum
#' @param MZHigh - List of maximum m/z values to be included in spectrum
#' @param RTLow - List of minimum retention time values for RT range of averaged spectrum
#' @param RTHigh - List of maximum retention time values for RT range of averaged spectrum
#' @param Profile - If TRUE data will presented in profile mode how is was acquired by mass spectrometer, If FALSE data will be presented in peak centroided mode
#' @return List of data frames of Mass and Intensities for requested averaged spectra
#' @examples
#' Coordinates for the glutamate peak observed in Figure 2A in reference paper
#' mz0 <- 148.0604342; dMz <- 0.002; d13C <- 1.0033548378;
#' Get two spectra in profile mode for isotopes envelope at 6th and 8th Minute
#' Spectra <- GetSpectrumArray(
#' rep("Thermo_QE_cells_72h_LA_1", 2),
#' rep(mz0 - 1,2),rep(mz0 + 5*d13C + 1,2),
#' c(6,8), c(7,9), TRUE)
#' @export
GetSpectrumArray =
function(FileNames,MZLows,MZHighs,RTLows,RTHighs,Profile=FALSE){
iface = get("iface", envir = WDSLEnvir)
ArAr=iface@functions$GetSpectrumArray(list(
FileNames=FileNames,
MZLow=MZLows,
MZHigh=MZHighs,
RTLow=RTLows,
RTHigh=RTHighs,
Profile=Profile))
if (is.character(ArAr@ErrorMessage)) print(ArAr@ErrorMessage)
Res=lapply(ArAr@GetSpectrumArrayResult,function(L){
data.frame(
Mass=L[c(TRUE,FALSE)],
Intensity=L[c(FALSE,TRUE)])})
return(Res)
}
#' Get total in certain LC-MS area.
#'
#' Gets sum of the signal for eXtracted Ion Current (XIC) chromatogram for specified LC-MS area.
#' Corresponds to mzAccess web-service API function GetTotal
#'
#' @param FileName - Name of original raw mass spectrometry file. Can be stated with or without path and extention
#' @param MZLow - Minimum m/z value for LC-MS area requested
#' @param MZHigh - Maximum m/z value for LC-MS area requested
#' @param RTLow - Minimum retention time value for LC-MS area requested
#' @param RTHigh - Maximum retention time value for LC-MS area requested
#' @param Cache - If TRUE data will be loaded from fast access cache, if FALSE - from original raw files
#' @return Double value of total ion current in for requested LC-MS area
#' @examples
#' GetTotal("Thermo_QE_cells_72h_LA_3",148.0584342,148.0624342,0,16)
#' @export
#' @import XML
#' @import XMLSchema
#' @import SSOAP
GetTotal =
function(FileName, MZLow, MZHigh, RTLow, RTHigh, Cache=TRUE){
iface = get("iface", envir = WDSLEnvir)
T1=iface@functions$GetTotal(list(
FileName=FileName,
MZLow=MZLow, MZHigh = MZHigh,
RTLow = RTLow, RTHigh = RTHigh ,
Cache=Cache))
if (is.character(T1@ErrorMessage)) print(T1@ErrorMessage)
L=T1@GetTotalResult
return(L)
}
#' Get Array of Totals for given LC-MS areas.
#'
#' Batch analog of GetTotal function.
#' Gets array of eXtracted Ion Current (XIC) chromatograms for specified LC-MS areas.
#' Equal length of incoming lists is assumed.
#' Corresponds to mzAccess web-service API function GetTotalArray
#'
#' @param FileNames - List of names of original raw mass spectrometry file.
#' @param MZLow - List of minimum m/z values for LC-MS areas requested
#' @param MZHigh - List of maximum m/z values for LC-MS areas requested
#' @param RTLow - List of minimum retention time values for LC-MS areas requested
#' @param RTHigh - List of maximum retention time values for LC-MS areas requested
#' @param Cache - If TRUE data will be loaded from fast access cache, if FALSE - from original raw files
#' @return List of doubles. Each n-th data frame represent single XIC chromatogram specified
#' by n-th members of incoming arrays and consist of
#' of Retention Time and Intensities for requested LC-MS area
#' @examples
#' Coordinates for the glutamate peak observed in Figure 2A in reference paper
#' mz0 <- 148.0604342; dMz <- 0.002; d13C <- 1.0033548378;rtMin <- 8; rtMax <- 9;
#' Get Totals for 1-st and 6-th isotopes
#'chrom <- GetTotalArray(
#' rep("Thermo_QE_cells_72h_LA_1", 2),
#' c(mz0-dMz, mz0 + 5*d13C - dMz),
#' c(mz0+dMz, mz0 + 5*d13C + dMz),
#' rep(rtMin, 2), rep(rtMax, 2))
#' @export
GetTotalArray =
function(FileNames,MZLows,MZHighs,RTLows,RTHighs,Cache=TRUE){
iface = get("iface", envir = WDSLEnvir)
Ar=iface@functions$GetTotalArray(list(
FileNames=FileNames,
MZLow=MZLows,
MZHigh=MZHighs,
RTLow=RTLows,
RTHigh=RTHighs,
Cache=Cache))
if (is.character(Ar@ErrorMessage)) print(Ar@ErrorMessage)
Res=Ar@GetTotalArrayResult
return(as.list(Res))
}
Yaroslav-Lyutvinskiy/MZAccessR documentation built on May 10, 2019, 12:06 a.m.
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# *******************************************************************************
# Copyright 2015-2017 Yaroslav Lyutvinskiy <Yaroslav.Lyutvinskiy@ki.se> and
# Roland Nilsson <Roland.Nilsson@ki.se>
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.using System;
#
# *******************************************************************************
setClass( 'ArrayOfArrayOfDouble' ,
representation(
.Data = 'list') ,
contains = c( 'list' ) )
setAs('XMLInternalElementNode', 'ArrayOfArrayOfDouble',
function (from, to = "ArrayOfArrayOfDouble", strict = TRUE)
xmlSApply(from, as, "ArrayOfDouble")
)
setClass( 'ArrayOfDouble' ,
representation(
.Data = 'numeric') ,
contains = c( 'numeric' ) )
setAs('XMLInternalElementNode', 'ArrayOfDouble',
function (from, to = "ArrayOfDouble", strict = TRUE)
xmlSApply(from, as, "numeric")
)
setAs('character', 'ArrayOfDouble',
function (from, to = "ArrayOfDouble", strict = TRUE)
new("ArrayOfDouble", as(from, "character"))
)
setAs('integer', 'ArrayOfDouble',
function (from, to = "ArrayOfDouble", strict = TRUE)
new("ArrayOfDouble", as(from, "integer"))
)
setAs('logical', 'ArrayOfDouble',
function (from, to = "ArrayOfDouble", strict = TRUE)
new("ArrayOfDouble", as(from, "logical"))
)
setClass( 'ArrayOfFragmentationInfo' ,
representation(
.Data = 'list') ,
contains = c( 'list' ) )
setAs('XMLInternalElementNode', 'ArrayOfFragmentationInfo',
function (from, to = "ArrayOfFragmentationInfo", strict = TRUE)
xmlSApply(from, as, "FragmentationInfo")
)
setClass( 'ArrayOfString' ,
representation(
.Data = 'character') ,
contains = c( 'character' ) )
setAs('XMLInternalElementNode', 'ArrayOfString',
function (from, to = "ArrayOfString", strict = TRUE)
xmlSApply(from, as, "character")
)
setAs('integer', 'ArrayOfString',
function (from, to = "ArrayOfString", strict = TRUE)
new("ArrayOfString", as(from, "integer"))
)
setAs('numeric', 'ArrayOfString',
function (from, to = "ArrayOfString", strict = TRUE)
new("ArrayOfString", as(from, "numeric"))
)
setAs('logical', 'ArrayOfString',
function (from, to = "ArrayOfString", strict = TRUE)
new("ArrayOfString", as(from, "logical"))
)
setClass( 'FileListResult.ErrorMessage' ,
representation(
FileListResult = 'ArrayOfString',
ErrorMessage = 'character') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'FileListResult.ErrorMessage',
function (from, to = "FileListResult.ErrorMessage", strict = TRUE)
coerceListToS4(from, new("FileListResult.ErrorMessage"))
)
setClass( 'FileName.Cache' ,
representation(
FileName = 'character',
Cache = 'logical') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'FileName.Cache',
function (from, to = "FileName.Cache", strict = TRUE)
coerceListToS4(from, new("FileName.Cache"))
)
setClass( 'FileName.MZLow.MZHigh.RT.Cache.Profile' ,
representation(
FileName = 'character',
MZLow = 'numeric',
MZHigh = 'numeric',
RT = 'numeric',
Cache = 'logical',
Profile = 'logical') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'FileName.MZLow.MZHigh.RT.Cache.Profile',
function (from, to = "FileName.MZLow.MZHigh.RT.Cache.Profile",
strict = TRUE)
coerceListToS4(from, new("FileName.MZLow.MZHigh.RT.Cache.Profile"))
)
setClass( 'FileName.MZLow.MZHigh.RTLow.RTHigh' ,
representation(
FileName = 'character',
MZLow = 'numeric',
MZHigh = 'numeric',
RTLow = 'numeric',
RTHigh = 'numeric') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'FileName.MZLow.MZHigh.RTLow.RTHigh',
function (from, to = "FileName.MZLow.MZHigh.RTLow.RTHigh", strict = TRUE)
coerceListToS4(from, new("FileName.MZLow.MZHigh.RTLow.RTHigh"))
)
setClass( 'FileName.MZLow.MZHigh.RTLow.RTHigh.Cache' ,
representation(
FileName = 'character',
MZLow = 'numeric',
MZHigh = 'numeric',
RTLow = 'numeric',
RTHigh = 'numeric',
Cache = 'logical') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'FileName.MZLow.MZHigh.RTLow.RTHigh.Cache',
function (from, to = "FileName.MZLow.MZHigh.RTLow.RTHigh.Cache",
strict = TRUE)
coerceListToS4(from, new("FileName.MZLow.MZHigh.RTLow.RTHigh.Cache"))
)
setClass( 'FileName.MZLow.MZHigh.RTLow.RTHigh.Cache.Profile' ,
representation(
FileName = 'character',
MZLow = 'numeric',
MZHigh = 'numeric',
RTLow = 'numeric',
RTHigh = 'numeric',
Cache = 'logical',
Profile = 'logical') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'FileName.MZLow.MZHigh.RTLow.RTHigh.Cache.Profile',
function (from, to = "FileName.MZLow.MZHigh.RTLow.RTHigh.Cache.Profile",
strict = TRUE)
coerceListToS4(from, new("FileName.MZLow.MZHigh.RTLow.RTHigh.Cache.Profile"))
)
setClass( 'FileName.MZLow.MZHigh.RTLow.RTHigh.Profile' ,
representation(
FileName = 'character',
MZLow = 'numeric',
MZHigh = 'numeric',
RTLow = 'numeric',
RTHigh = 'numeric',
Profile = 'logical') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'FileName.MZLow.MZHigh.RTLow.RTHigh.Profile',
function (from, to = "FileName.MZLow.MZHigh.RTLow.RTHigh.Profile",
strict = TRUE)
coerceListToS4(from, new("FileName.MZLow.MZHigh.RTLow.RTHigh.Profile"))
)
setClass( 'FileName.MZLow.MZHigh.ScanNumber.Cache.Profile' ,
representation(
FileName = 'character',
MZLow = 'numeric',
MZHigh = 'numeric',
ScanNumber = 'integer',
Cache = 'logical',
Profile = 'logical') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'FileName.MZLow.MZHigh.ScanNumber.Cache.Profile',
function (from, to = "FileName.MZLow.MZHigh.ScanNumber.Cache.Profile",
strict = TRUE)
coerceListToS4(from, new("FileName.MZLow.MZHigh.ScanNumber.Cache.Profile"))
)
setClass( 'FileName.RT.Cache' ,
representation(
FileName = 'character',
RT = 'numeric',
Cache = 'logical') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'FileName.RT.Cache',
function (from, to = "FileName.RT.Cache", strict = TRUE)
coerceListToS4(from, new("FileName.RT.Cache"))
)
setClass( 'FileName.ScanNumber.Cache' ,
representation(
FileName = 'character',
ScanNumber = 'integer',
Cache = 'logical') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'FileName.ScanNumber.Cache',
function (from, to = "FileName.ScanNumber.Cache", strict = TRUE)
coerceListToS4(from, new("FileName.ScanNumber.Cache"))
)
setClass( 'FileNames.MZLow.MZHigh.RTLow.RTHigh.Cache' ,
representation(
FileNames = 'ArrayOfString',
MZLow = 'ArrayOfDouble',
MZHigh = 'ArrayOfDouble',
RTLow = 'ArrayOfDouble',
RTHigh = 'ArrayOfDouble',
Cache = 'logical') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'FileNames.MZLow.MZHigh.RTLow.RTHigh.Cache',
function (from, to = "FileNames.MZLow.MZHigh.RTLow.RTHigh.Cache", strict = TRUE)
coerceListToS4(from, new("FileNames.MZLow.MZHigh.RTLow.RTHigh.Cache"))
)
setClass( 'FileNames.MZLow.MZHigh.RTLow.RTHigh.Cache.Profile' ,
representation(
FileNames = 'ArrayOfString',
MZLow = 'ArrayOfDouble',
MZHigh = 'ArrayOfDouble',
RTLow = 'ArrayOfDouble',
RTHigh = 'ArrayOfDouble',
Cache = 'logical',
Profile = 'logical') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'FileNames.MZLow.MZHigh.RTLow.RTHigh.Cache.Profile',
function (from, to = "FileNames.MZLow.MZHigh.RTLow.RTHigh.Cache.Profile", strict = TRUE)
coerceListToS4(from, new("FileNames.MZLow.MZHigh.RTLow.RTHigh.Cache.Profile"))
)
setClass( 'FileNames.MZLow.MZHigh.RTLow.RTHigh.Profile' ,
representation(
FileNames = 'ArrayOfString',
MZLow = 'ArrayOfDouble',
MZHigh = 'ArrayOfDouble',
RTLow = 'ArrayOfDouble',
RTHigh = 'ArrayOfDouble',
Profile = 'logical') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'FileNames.MZLow.MZHigh.RTLow.RTHigh.Profile',
function (from, to = "FileNames.MZLow.MZHigh.RTLow.RTHigh.Profile", strict = TRUE)
coerceListToS4(from, new("FileNames.MZLow.MZHigh.RTLow.RTHigh.Profile"))
)
setClass( 'FragmentationInfo' ,
representation(
RT = 'numeric',
ParentMZ = 'numeric',
ScanNumber = 'integer',
MSOrder = 'integer',
Description = 'character') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'FragmentationInfo',
function (from, to = "FragmentationInfo", strict = TRUE)
coerceListToS4(from, new("FragmentationInfo"))
)
setClass( 'GetAreaArrayResult.ErrorMessage' ,
representation(
GetAreaArrayResult = 'ArrayOfArrayOfDouble',
ErrorMessage = 'character') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'GetAreaArrayResult.ErrorMessage',
function (from, to = "GetAreaArrayResult.ErrorMessage", strict = TRUE)
coerceListToS4(from, new("GetAreaArrayResult.ErrorMessage"))
)
setClass( 'GetAreaResult.ErrorMessage' ,
representation(
GetAreaResult = 'ArrayOfDouble',
ErrorMessage = 'character') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'GetAreaResult.ErrorMessage',
function (from, to = "GetAreaResult.ErrorMessage", strict = TRUE)
coerceListToS4(from, new("GetAreaResult.ErrorMessage"))
)
setClass( 'GetAverageSpectrumResult.ErrorMessage' ,
representation(
GetAverageSpectrumResult = 'ArrayOfDouble',
ErrorMessage = 'character') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'GetAverageSpectrumResult.ErrorMessage',
function (from, to = "GetAverageSpectrumResult.ErrorMessage", strict = TRUE)
coerceListToS4(from, new("GetAverageSpectrumResult.ErrorMessage"))
)
setClass( 'GetChromatogramArrayResult.ErrorMessage' ,
representation(
GetChromatogramArrayResult = 'ArrayOfArrayOfDouble',
ErrorMessage = 'character') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'GetChromatogramArrayResult.ErrorMessage',
function (from, to = "GetChromatogramArrayResult.ErrorMessage", strict = TRUE)
coerceListToS4(from, new("GetChromatogramArrayResult.ErrorMessage"))
)
setClass( 'GetChromatogramResult.ErrorMessage' ,
representation(
GetChromatogramResult = 'ArrayOfDouble',
ErrorMessage = 'character') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'GetChromatogramResult.ErrorMessage',
function (from, to = "GetChromatogramResult.ErrorMessage", strict = TRUE)
coerceListToS4(from, new("GetChromatogramResult.ErrorMessage"))
)
setClass( 'GetFragmentationEventsResult.ErrorMessage' ,
representation(
GetFragmentationEventsResult = 'ArrayOfFragmentationInfo',
ErrorMessage = 'character') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'GetFragmentationEventsResult.ErrorMessage',
function (from, to = "GetFragmentationEventsResult.ErrorMessage", strict = TRUE)
coerceListToS4(from, new("GetFragmentationEventsResult.ErrorMessage"))
)
setClass( 'GetMZRangeResult.ErrorMessage' ,
representation(
GetMZRangeResult = 'ArrayOfDouble',
ErrorMessage = 'character') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'GetMZRangeResult.ErrorMessage',
function (from, to = "GetMZRangeResult.ErrorMessage", strict = TRUE)
coerceListToS4(from, new("GetMZRangeResult.ErrorMessage"))
)
setClass( 'GetRTFromScanNumberResult.ErrorMessage' ,
representation(
GetRTFromScanNumberResult = 'numeric',
ErrorMessage = 'character') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'GetRTFromScanNumberResult.ErrorMessage',
function (from, to = "GetRTFromScanNumberResult.ErrorMessage",
strict = TRUE)
coerceListToS4(from, new("GetRTFromScanNumberResult.ErrorMessage"))
)
setClass( 'GetRTRangeResult.ErrorMessage' ,
representation(
GetRTRangeResult = 'ArrayOfDouble',
ErrorMessage = 'character') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'GetRTRangeResult.ErrorMessage',
function (from, to = "GetRTRangeResult.ErrorMessage", strict = TRUE)
coerceListToS4(from, new("GetRTRangeResult.ErrorMessage"))
)
setClass( 'GetScanNumberFromRTResult.ErrorMessage' ,
representation(
GetScanNumberFromRTResult = 'integer',
ErrorMessage = 'character') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'GetScanNumberFromRTResult.ErrorMessage',
function (from, to = "GetScanNumberFromRTResult.ErrorMessage",
strict = TRUE)
coerceListToS4(from, new("GetScanNumberFromRTResult.ErrorMessage"))
)
setClass( 'GetSpectraArrayResult.ErrorMessage' ,
representation(
GetSpectraArrayResult = 'ArrayOfArrayOfDouble',
ErrorMessage = 'character') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'GetSpectraArrayResult.ErrorMessage',
function (from, to = "GetSpectraArrayResult.ErrorMessage", strict = TRUE)
coerceListToS4(from, new("GetSpectraArrayResult.ErrorMessage"))
)
setClass( 'GetSpectrumbyRTResult.ErrorMessage' ,
representation(
GetSpectrumbyRTResult = 'ArrayOfDouble',
ErrorMessage = 'character') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'GetSpectrumbyRTResult.ErrorMessage',
function (from, to = "GetSpectrumbyRTResult.ErrorMessage", strict = TRUE)
coerceListToS4(from, new("GetSpectrumbyRTResult.ErrorMessage"))
)
setClass( 'GetSpectrumbyScanNumberResult.ErrorMessage' ,
representation(
GetSpectrumbyScanNumberResult = 'ArrayOfDouble',
ErrorMessage = 'character') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'GetSpectrumbyScanNumberResult.ErrorMessage',
function (from, to = "GetSpectrumbyScanNumberResult.ErrorMessage",
strict = TRUE)
coerceListToS4(from, new("GetSpectrumbyScanNumberResult.ErrorMessage"))
)
setClass( 'GetTotalArrayResult.ErrorMessage' ,
representation(
GetTotalArrayResult = 'ArrayOfDouble',
ErrorMessage = 'character') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'GetTotalArrayResult.ErrorMessage',
function (from, to = "GetTotalArrayResult.ErrorMessage", strict = TRUE)
coerceListToS4(from, new("GetTotalArrayResult.ErrorMessage"))
)
setClass( 'GetTotalResult.ErrorMessage' ,
representation(
GetTotalResult = 'numeric',
ErrorMessage = 'character') ,
contains = c( 'VirtualSOAPClass' ) )
setAs('list', 'GetTotalResult.ErrorMessage',
function (from, to = "GetTotalResult.ErrorMessage", strict = TRUE)
coerceListToS4(from, new("GetTotalResult.ErrorMessage")))
setMethod("toSOAP", c("logical", "XMLInternalElementNode", type = "PrimitiveSOAPType"),
function(obj, con = xmlOutputBuffer(header=""), type = NULL, literal = FALSE, elementFormQualified = FALSE, ...)
{
if (literal){
if (.Primitive("as.logical")(obj)) {
newXMLTextNode("true",parent=con)
}
else {
newXMLTextNode("false",parent = con)
}
}else{
if (.Primitive("as.logical")(obj))
"true"
else
"false"
}
})
setAs('list', 'ArrayOfDouble',
function (from, to = "ArrayOfDouble", strict = TRUE)
new("ArrayOfDouble", as(from, "list")))
setAs('list', 'ArrayOfString',
function (from, to = "ArrayOfString", strict = TRUE)
new("ArrayOfString", as(from, "list")))
setAs('matrix', 'ArrayOfArrayOfDouble',
function (from, to = "ArrayOfArrayOfDouble", strict = TRUE){
Res = new("ArrayOfArrayOfDouble")
for(i in 1:dim(from)[2]){
Res[[i]]=from[,i]
}
Res
})
#' @export
MZRange <- setClass("MZRange", slots = c(MinMZ="numeric", MaxMZ="numeric"))
#' @export
RTRange <- setClass("RTRange", slots = c(MinRT="numeric", MaxRT="numeric"))
#' @export
LCMSArea <- setClass("LCMSArea", slots = c(RTRange="RTRange", MZRange="MZRange"))
WDSLEnvir = new.env()
#' Setup for Web-server
#'
#' Checks server connection and loads function prototypes.
#' All other functions become working only afrter SetupServer call.
#'
#' @param ServerURL - WDSL page of mzAccess web server
#' @return None
#' @examples
#' SetupServer()
#' @export
SetupServer =
function(ServerURL = "http://charon.ad.cmm.se:6060/MzAccessPublicTest/Service.asmx?WSDL"){
wsdl = processWSDL(ServerURL)
assign("wsdl", wsdl, envir = WDSLEnvir)
iface= genSOAPClientInterface(wsdl)
assign("iface", iface, envir = WDSLEnvir)
}
#' Get XIC Chromatogram
#'
#' Gets eXtracted Ion Current (XIC) chromatograms for specified LC-MS area.
#' Corresponds to mzAccess web-service API function GetChromatogram
#'
#' @param FileName - Name of original raw mass spectrometry file. Can be stated with or without path and extention
#' @param MZLow - Minimum m/z value for LC-MS area requested
#' @param MZHigh - Maximum m/z value for LC-MS area requested
#' @param RTLow - Minimum retention time value for LC-MS area requested
#' @param RTHigh - Maximum retention time value for LC-MS area requested
#' @param Cache - If TRUE data will be loaded from fast access cache, if FALSE - from original raw files
#' @return Data frame of Retention Time and Intensities for requested LC-MS area
#' @examples
#' GetChromatogram("Thermo_QE_cells_72h_LA_3",148.0584342,148.0624342,0,16)
#' @export
#' @import XML
#' @import XMLSchema
#' @import SSOAP
GetChromatogram =
function(FileName, MZLow, MZHigh, RTLow, RTHigh, Cache=TRUE){
iface = get("iface", envir = WDSLEnvir)
CH1=iface@functions$GetChromatogram(list(
FileName=FileName,
MZLow=MZLow, MZHigh = MZHigh,
RTLow = RTLow, RTHigh = RTHigh ,
Cache=Cache))
if (is.character(CH1@ErrorMessage)) print(CH1@ErrorMessage)
L=CH1@GetChromatogramResult
CHR=data.frame(RT=L[c(TRUE,FALSE)],Intensity=L[c(FALSE,TRUE)])
return(CHR)
}
#' Get LC-MS Area signals
#'
#' Gets all non-zero signals for specified LC-MS area.
#' Corresponds to mzAccess web-service API function GetArea
#'
#' @param FileName - Name of original raw mass spectrometry file. Can be stated with or without path and extention
#' @param MZLow - Minimum m/z value for LC-MS area requested
#' @param MZHigh - Maximum m/z value for LC-MS area requested
#' @param RTLow - Minimum retention time value for LC-MS area requested
#' @param RTHigh - Maximum retention time value for LC-MS area requested
#' @param Cache - If TRUE data will be loaded from fast access cache, if FALSE - from original raw files
#' @param Profile - If TRUE data will presented in profile mode how is was acquired by mass spectrometer, If FALSE data will be presented in peak centroided mode
#' @return Data frame of Mass, Retention Time and Intensities for requested LC-MS area
#' @examples
#' GetArea(FileName="Thermo_QE_cells_72h_UL_1",149.047,149.074, RTLow = 8.2, RTHigh = 8.5,Profile = TRUE, Cache = FALSE)
#' @export
GetArea =
function(FileName, MZLow, MZHigh, RTLow, RTHigh, Cache=TRUE, Profile = FALSE){
iface = get("iface", envir = WDSLEnvir)
Ar=iface@functions$GetArea(list(
FileName=FileName,
MZLow=MZLow, MZHigh = MZHigh,
RTLow = RTLow, RTHigh = RTHigh ,
Cache=Cache, Profile = Profile))
if (is.character(Ar@ErrorMessage)) print(Ar@ErrorMessage)
L=Ar@GetAreaResult
AREA=data.frame(Mass=L[c(TRUE,FALSE,FALSE)],RT=L[c(FALSE,TRUE,FALSE)],Intensity=L[c(FALSE,FALSE,TRUE)])
return(AREA)
}
#' Get averaged spectrum
#'
#' Get spectrum averaged (or summed) within RT interval
#' Corresponds to mzAccess web-service API function GetAverageSpectrum
#' Averaging algorithm is vendor specific, therefore function has no cache option
#'
#' @param FileName - Name of original raw mass spectrometry file. Can be stated with or without path and extention
#' @param MZLow - Minimum m/z value to be included in spectrum
#' @param MZHigh - Maximum m/z value to be included in spectrum
#' @param RTLow - Minimum retention time value for RT range of averaged spectrum
#' @param RTHigh - Maximum retention time value for RT range of averaged spectrum
#' @param Profile - If TRUE data will presented in profile mode how is was acquired by mass spectrometer, If FALSE data will be presented in peak centroided mode
#' @return Data frame of Mass and Intensities for requested LC-MS area
#' @examples
#' GetAvgSpectrum("Thermo_QE_cells_72h_LA_3", MZLow = 50, MZHigh = 400, RTLow = 6, RTHigh = 8, Profile = FALSE)
#' @export
GetAvgSpectrum =
function(FileName, MZLow, MZHigh, RTLow, RTHigh, Profile = FALSE){
iface = get("iface", envir = WDSLEnvir)
Sp=iface@functions$GetAverageSpectrum(list(
FileName=FileName,
MZLow=MZLow, MZHigh = MZHigh,
RTLow = RTLow, RTHigh = RTHigh ,
Profile = Profile))
if (is.character(Sp@ErrorMessage)) print(Sp@ErrorMessage)
L=Sp@GetAverageSpectrumResult
SPC=data.frame(Mass=L[c(TRUE,FALSE)],Intensity=L[c(FALSE,TRUE)])
return(SPC)
}
#' Get spectrum for RT
#'
#' Get Single scan spectrum on certain RT.
#' Web-service will provide first spectrum where RT is not less than specified
#' Corresponds to mzAccess web-service API function GetSpectrumbyRT
#'
#' @param FileName - Name of original raw mass spectrometry file. Can be stated with or without path and extention
#' @param MZLow - Minimum m/z value to be included in spectrum
#' @param MZHigh - Maximum m/z value to be included in spectrum
#' @param RT - retention time for which spectrum will be searched.
#' @param Cache - If TRUE data will be loaded from fast access cache, if FALSE - from original raw files
#' @param Profile - If TRUE data will presented in profile mode how is was acquired by mass spectrometer, If FALSE data will be presented in peak centroided mode
#' @return Data frame of Mass and Intensities for requested LC-MS area
#' @examples
#' GetSpectrumByRT("Thermo_QE_cells_72h_LA_3", MZLow = 50, MZHigh = 400, RT = 6, Cache = FALSE, Profile = FALSE)
#' @export
GetSpectrumByRT =
function(FileName, MZLow, MZHigh, RT, Cache=FALSE, Profile = FALSE){
iface = get("iface", envir = WDSLEnvir)
Sp=iface@functions$GetSpectrumByRT(list(
FileName=FileName,
MZLow=MZLow, MZHigh = MZHigh,
RT = RT,
Cache=Cache, Profile = Profile))
if (is.character(Sp@ErrorMessage)) print(Sp@ErrorMessage)
L=Sp@GetSpectrumByRTResult
SPC=data.frame(Mass=L[c(TRUE,FALSE)],Intensity=L[c(FALSE,TRUE)])
return(SPC)
}
#' Get spectrum for scan number
#'
#' Get Single scan spectrum for certain scan.
#' Corresponds to mzAccess web-service API function GetSpectrumbyScanNumber
#'
#' @param FileName - Name of original raw mass spectrometry file. Can be stated with or without path and extention
#' @param MZLow - Minimum m/z value to be included in spectrum
#' @param MZHigh - Maximum m/z value to be included in spectrum
#' @param ScanNumber - scan number for requested spectrum.
#' @param Profile - If TRUE data will presented in profile mode how is was acquired by mass spectrometer, If FALSE data will be presented in peak centroided mode
#' @param Cache - If TRUE data will be loaded from fast access cache, if FALSE - from original raw files
#' @return Data frame of Mass and Intensities for requested LC-MS area
#' @examples
#' GetSpectrumByScanNumber("Thermo_QE_cells_72h_LA_3", MZLow = 50, MZHigh = 400, ScanNumber = 1000, Profile = TRUE)
#' @export
GetSpectrumByScanNumber =
function(FileName, MZLow, MZHigh, ScanNumber, Cache=FALSE, Profile = FALSE){
iface = get("iface", envir = WDSLEnvir)
Sp=iface@functions$GetSpectrumByScanNumber(list(
FileName=FileName,
MZLow=MZLow, MZHigh = MZHigh,
ScanNumber = ScanNumber,
Cache=Cache, Profile = Profile))
if (is.character(Sp@ErrorMessage)) print(Sp@ErrorMessage)
L=Sp@GetSpectrumByScanNumberResult
SPC=data.frame(Mass=L[c(TRUE,FALSE)],Intensity=L[c(FALSE,TRUE)])
return(SPC)
}
#' Get scan number for retention time
#'
#' Get scan number
#' Corresponds to mzAccess web-service API function GetScanNumberFromRT
#' Web-service will provide first scan number where RT is not less than specified
#'
#' @param FileName - Name of original raw mass spectrometry file. Can be stated with or without path and extention
#' @param RT - retention time for which spectrum will be searched.
#' @param Cache - If TRUE scan number will be loaded from fast access cache, if FALSE - from original raw files
#' @return Interger scan number
#' @examples
#' GetScanNumberFromRT("Thermo_QE_cells_72h_LA_3",6)
#' @export
GetScanNumberFromRT =
function(FileName, RT, Cache=FALSE){
iface = get("iface", envir = WDSLEnvir)
Scan=iface@functions$GetScanNumberFromRT(list(
FileName=FileName,
RT = RT, Cache=Cache))
if (is.character(Scan@ErrorMessage)) print(Scan@ErrorMessage)
L=Scan@GetScanNumberFromRTResult
return(L)
}
#' Get retention time for scan number
#'
#' Get retention time for scan number
#' Corresponds to mzAccess web-service API function GetRTFromScanNumber
#' Web-service will provide first scan number where RT is not less than specified
#'
#' @param FileName - Name of original raw mass spectrometry file. Can be stated with or without path and extention
#' @param RT - retention time for which spectrum will be searched.
#' @param Cache - If TRUE retention time value (in minutes) will be loaded from fast access cache, if FALSE - from original raw files
#' @return Retention time value
#' @examples
#' GetRTFromScanNumber("Thermo_QE_cells_72h_LA_3",1000)
#' @export
GetRTFromScanNumber =
function(FileName, ScanNumber, Cache=FALSE){
iface = get("iface", envir = WDSLEnvir)
RT=iface@functions$GetRTFromScanNumber(list(
FileName=FileName,
ScanNumber = ScanNumber, Cache=Cache))
if (is.character(RT@ErrorMessage)) print(RT@ErrorMessage)
L=RT@GetRTFromScanNumberResult
return(L)
}
#' Get mass range for spectra in file
#'
#' Get mass range for spectra in file
#' Corresponds to mzAccess web-service API function GetMZRange
#'
#' @param FileName - Name of original raw mass spectrometry file. Can be stated with or without path and extention
#' @param Cache - If TRUE Mass Range will show minimum amd maximim masses avialable in spectra through the file, if FALSE - it will return Mass Interval where masses were scanned by mass spectrometer
#' @return MassRange object with slots MinMZ,MaxMZ
#' @examples
#' GetMZRange("Thermo_QE_cells_72h_LA_3")
#' @export
GetMZRange =
function(FileName, Cache=FALSE){
iface = get("iface", envir = WDSLEnvir)
Range=iface@functions$GetMZRange(
list(FileName=FileName, Cache=Cache))
if (is.character(Range@ErrorMessage)) print(Range@ErrorMessage)
R=MZRange(MinMZ=Range@GetMZRangeResult[1],
MaxMZ=Range@GetMZRangeResult[2])
return(R)
}
#' Get retention time range for spectra in file
#'
#' Get retention time range for spectra in file
#' Corresponds to mzAccess web-service API function GetRTRange
#'
#' @param FileName - Name of original raw mass spectrometry file. Can be stated with or without path and extention
#' @param Cache - If TRUE RT Range will show RTs for first and last spectra in spectra through the file, if FALSE - it will retention time range as registered by mass spectrometer
#' @return RTRange object with slots MinRT,MaxRT
#' @examples
#' GetRTRange("Thermo_QE_cells_72h_LA_3")
#' @export
GetRTRange =
function(FileName, Cache=FALSE){
iface = get("iface", envir = WDSLEnvir)
Range=iface@functions$GetRTRange(
list(FileName=FileName, Cache=Cache))
if (is.character(Range@ErrorMessage)) print(Range@ErrorMessage)
R=RTRange(MinRT=Range@GetRTRangeResult[1],
MaxRT=Range@GetRTRangeResult[2])
return(R)
}
#' Get list of avialable files
#'
#' Get list of avialable files by provided mask
#' Corresponds to mzAccess web-service API function FileList
#'
#' @param FileMask - File mask for file search Applied to file name only without extension. Case insensitive. Can contain "*"and "?" mask symbols
#' @return List of available file names
#' @examples
#' FileList("*72h*")
#' @export
FileList =
function(FileMask = "*"){
iface = get("iface", envir = WDSLEnvir)
FList =iface@functions$FileList(FileMask)
if (is.character(FList@ErrorMessage)) print(FList@ErrorMessage)
L = FList@FileListResult@.Data
return(as.list(L))
}
#' Get data frame of fragmentation events in requested LC-MS area
#'
#' Get data frame of fragmentation events in requested LC-MS area
#' Corresponds to mzAccess web-service API function GetFragmentationEvents
#'
#' @param FileName - Name of original raw mass spectrometry file.
#' @param MZLow - Minimum parent ion m/z value to be included in event list
#' @param MZHigh - Maximum parent ion m/z value to be included in event list
#' @param RTLow - Minimum retention time value to be included in event list
#' @param RTHigh - Maximum retention time value to be included in event list
#' @return Data frame of fragmentation events inside of desired LC-MS region
#' Includes Scan Number (to use with function GetSpectraByScanNumber),
#' Mass of parent ion,
#' Retention time of fragmentation event
#' MSOrder - if 2 - that is MSMS spectra, if more it is high order MSN spectra
#' Desc - description of spectrum
#' @examples
#' GetFragmentationEvents("Agilent_QTOF_plasma_1.d",200,250,6,6.5)
#' @export
GetFragmentationEvents =
function(FileName, MZLow, MZHigh, RTLow, RTHigh){
iface = get("iface", envir = WDSLEnvir)
SPInfo = iface@functions$GetFragmentationEvents(list(
FileName=FileName,
MZLow = MZLow, MZHigh = MZHigh,
RTLow = RTLow, RTHigh = RTHigh))
if (is.character(SPInfo@ErrorMessage)) print(SPInfo@ErrorMessage)
df = data.frame(
ScanNumber=as.numeric(sapply(SPInfo@GetFragmentationEventsResult,function(x)x@ScanNumber,simplify = TRUE )),
ParentMZ=as.numeric(sapply(SPInfo@GetFragmentationEventsResult,function(x)x@ParentMZ,simplify = TRUE )),
RT=as.numeric(sapply(SPInfo@GetFragmentationEventsResult,function(x)x@RT,simplify = TRUE )),
MSOrder=as.numeric(sapply(SPInfo@GetFragmentationEventsResult,function(x)x@MSOrder,simplify = TRUE )),
Description = as.character(sapply(SPInfo@GetFragmentationEventsResult,function(x)x@Description,simplify = TRUE ))
)
return(df)
}
#' Get Array of XIC Chromatogram
#'
#' Batch analog of GetChromatogram function.
#' Gets array of eXtracted Ion Current (XIC) chromatograms for specified LC-MS areas.
#' Equal length of incoming lists is assumed.
#' Corresponds to mzAccess web-service API function GetChromatogramsArray
#'
#' @param FileNames - List of names of original raw mass spectrometry file.
#' @param MZLow - List of minimum m/z values for LC-MS areas requested
#' @param MZHigh - List of maximum m/z values for LC-MS areas requested
#' @param RTLow - List of minimum retention time values for LC-MS areas requested
#' @param RTHigh - List of maximum retention time values for LC-MS areas requested
#' @param Cache - If TRUE data will be loaded from fast access cache, if FALSE - from original raw files
#' @return List of data frames. Each n-th data frame represent single XIC chromatogram specified
#' by n-th members of incoming arrays and consist of
#' of Retention Time and Intensities for requested LC-MS area
#' @examples
#' Coordinates for the glutamate peak observed in Figure 2A in reference paper
#' mz0 <- 148.0604342; dMz <- 0.002; d13C <- 1.0033548378;rtMin <- 8; rtMax <- 9;
#' Get Chromatograms for 1-st and 6-th isotopes
#'chrom <- GetChromatogramArray(
#' rep("Thermo_QE_cells_72h_LA_1", 2),
#' c(mz0-dMz, mz0 + 5*d13C - dMz),
#' c(mz0+dMz, mz0 + 5*d13C + dMz),
#' rep(rtMin, 2), rep(rtMax, 2))
#' @export
GetChromatogramArray =
function(FileNames,MZLows,MZHighs,RTLows,RTHighs,Cache=TRUE){
iface = get("iface", envir = WDSLEnvir)
ArAr=iface@functions$GetChromatogramArray(list(
FileNames=FileNames,
MZLow=MZLows,
MZHigh=MZHighs,
RTLow=RTLows,
RTHigh=RTHighs,
Cache=Cache))
if (is.character(ArAr@ErrorMessage)) print(ArAr@ErrorMessage)
Res=lapply(ArAr@GetChromatogramArrayResult,function(L){
data.frame(
RT=L[c(TRUE,FALSE)],
Intensity=L[c(FALSE,TRUE)])})
return(Res)
}
#' Get Array of LC-MS Area signals
#'
#' Batch analog of GetArea function.
#' Gets List of data frames where each data frame contains all non-zero signals for one of specified LC-MS areas.
#' Equal length of incoming lists is assumed.
#' Corresponds to mzAccess web-service API function GetAreasArray
#'
#' @param FileNames - List of names of original raw mass spectrometry file.
#' @param MZLow - List of minimum m/z values for LC-MS areas requested
#' @param MZHigh - List of maximum m/z values for LC-MS areas requested
#' @param RTLow - List of minimum retention time values for LC-MS areas requested
#' @param RTHigh - List of maximum retention time values for LC-MS areas requested
#' @param Cache - If TRUE data will be loaded from fast access cache, if FALSE - from original raw files
#' @param Profile - If TRUE data will presented in profile mode how is was acquired by mass spectrometer, If FALSE data will be presented in peak centroided mode
#' @return List of data frames. Each n-th data frame contains Mass, Retention Time and Intensities for all non-zero signals for LC-MS area, specified
#' by n-th members of incoming arrays.
#' @examples
#' Coordinates for the glutamate peak observed in Figure 2A in reference paper
#' mz0 <- 148.0604342; dMz <- 0.002; d13C <- 1.0033548378;rtMin <- 8; rtMax <- 9;
#' Get MZ/RT areas for 1-st and 6-th isotopes
#' Areas <- GetAreaArray(
#' rep("Thermo_QE_cells_72h_LA_1", 2),
#' c(mz0-dMz, mz0 + 5*d13C - dMz),
#' c(mz0+dMz, mz0 + 5*d13C + dMz),
#' rep(rtMin, 2), rep(rtMax, 2))
#' @export
GetAreaArray =
function(FileNames,MZLows,MZHighs,RTLows,RTHighs,Cache=TRUE,Profile=FALSE){
iface = get("iface", envir = WDSLEnvir)
ArAr=iface@functions$GetAreaArray(list(
FileNames=FileNames,
MZLow=MZLows,
MZHigh=MZHighs,
RTLow=RTLows,
RTHigh=RTHighs,
Cache=Cache,
Profile=Profile))
if (is.character(ArAr@ErrorMessage)) print(ArAr@ErrorMessage)
Res=lapply(ArAr@GetAreaArrayResult,function(L){
data.frame(
Mass=L[c(TRUE,FALSE,FALSE)],
RT=L[c(FALSE,TRUE,FALSE)],
Intensity=L[c(FALSE,FALSE,TRUE)])})
return(Res)
}
#' Get Array of averaged spectra
#'
#' Batch analog of GetAveSpectrum function.
#' Get Array of spectra averaged (or summed) within desired RT intervals
#' Corresponds to mzAccess web-service API function GetSpectrumArray
#' Equal length of incoming lists is assumed.
#' Averaging algorithm is vendor specific, therefore function has no cache option
#'
#' @param FileName - Name of original raw mass spectrometry file. Can be stated with or without path and extention
#' @param MZLow - List of minimum m/z values to be included in spectrum
#' @param MZHigh - List of maximum m/z values to be included in spectrum
#' @param RTLow - List of minimum retention time values for RT range of averaged spectrum
#' @param RTHigh - List of maximum retention time values for RT range of averaged spectrum
#' @param Profile - If TRUE data will presented in profile mode how is was acquired by mass spectrometer, If FALSE data will be presented in peak centroided mode
#' @return List of data frames of Mass and Intensities for requested averaged spectra
#' @examples
#' Coordinates for the glutamate peak observed in Figure 2A in reference paper
#' mz0 <- 148.0604342; dMz <- 0.002; d13C <- 1.0033548378;
#' Get two spectra in profile mode for isotopes envelope at 6th and 8th Minute
#' Spectra <- GetSpectrumArray(
#' rep("Thermo_QE_cells_72h_LA_1", 2),
#' rep(mz0 - 1,2),rep(mz0 + 5*d13C + 1,2),
#' c(6,8), c(7,9), TRUE)
#' @export
GetSpectrumArray =
function(FileNames,MZLows,MZHighs,RTLows,RTHighs,Profile=FALSE){
iface = get("iface", envir = WDSLEnvir)
ArAr=iface@functions$GetSpectrumArray(list(
FileNames=FileNames,
MZLow=MZLows,
MZHigh=MZHighs,
RTLow=RTLows,
RTHigh=RTHighs,
Profile=Profile))
if (is.character(ArAr@ErrorMessage)) print(ArAr@ErrorMessage)
Res=lapply(ArAr@GetSpectrumArrayResult,function(L){
data.frame(
Mass=L[c(TRUE,FALSE)],
Intensity=L[c(FALSE,TRUE)])})
return(Res)
}
#' Get total in certain LC-MS area.
#'
#' Gets sum of the signal for eXtracted Ion Current (XIC) chromatogram for specified LC-MS area.
#' Corresponds to mzAccess web-service API function GetTotal
#'
#' @param FileName - Name of original raw mass spectrometry file. Can be stated with or without path and extention
#' @param MZLow - Minimum m/z value for LC-MS area requested
#' @param MZHigh - Maximum m/z value for LC-MS area requested
#' @param RTLow - Minimum retention time value for LC-MS area requested
#' @param RTHigh - Maximum retention time value for LC-MS area requested
#' @param Cache - If TRUE data will be loaded from fast access cache, if FALSE - from original raw files
#' @return Double value of total ion current in for requested LC-MS area
#' @examples
#' GetTotal("Thermo_QE_cells_72h_LA_3",148.0584342,148.0624342,0,16)
#' @export
#' @import XML
#' @import XMLSchema
#' @import SSOAP
GetTotal =
function(FileName, MZLow, MZHigh, RTLow, RTHigh, Cache=TRUE){
iface = get("iface", envir = WDSLEnvir)
T1=iface@functions$GetTotal(list(
FileName=FileName,
MZLow=MZLow, MZHigh = MZHigh,
RTLow = RTLow, RTHigh = RTHigh ,
Cache=Cache))
if (is.character(T1@ErrorMessage)) print(T1@ErrorMessage)
L=T1@GetTotalResult
return(L)
}
#' Get Array of Totals for given LC-MS areas.
#'
#' Batch analog of GetTotal function.
#' Gets array of eXtracted Ion Current (XIC) chromatograms for specified LC-MS areas.
#' Equal length of incoming lists is assumed.
#' Corresponds to mzAccess web-service API function GetTotalArray
#'
#' @param FileNames - List of names of original raw mass spectrometry file.
#' @param MZLow - List of minimum m/z values for LC-MS areas requested
#' @param MZHigh - List of maximum m/z values for LC-MS areas requested
#' @param RTLow - List of minimum retention time values for LC-MS areas requested
#' @param RTHigh - List of maximum retention time values for LC-MS areas requested
#' @param Cache - If TRUE data will be loaded from fast access cache, if FALSE - from original raw files
#' @return List of doubles. Each n-th data frame represent single XIC chromatogram specified
#' by n-th members of incoming arrays and consist of
#' of Retention Time and Intensities for requested LC-MS area
#' @examples
#' Coordinates for the glutamate peak observed in Figure 2A in reference paper
#' mz0 <- 148.0604342; dMz <- 0.002; d13C <- 1.0033548378;rtMin <- 8; rtMax <- 9;
#' Get Totals for 1-st and 6-th isotopes
#'chrom <- GetTotalArray(
#' rep("Thermo_QE_cells_72h_LA_1", 2),
#' c(mz0-dMz, mz0 + 5*d13C - dMz),
#' c(mz0+dMz, mz0 + 5*d13C + dMz),
#' rep(rtMin, 2), rep(rtMax, 2))
#' @export
GetTotalArray =
function(FileNames,MZLows,MZHighs,RTLows,RTHighs,Cache=TRUE){
iface = get("iface", envir = WDSLEnvir)
Ar=iface@functions$GetTotalArray(list(
FileNames=FileNames,
MZLow=MZLows,
MZHigh=MZHighs,
RTLow=RTLows,
RTHigh=RTHighs,
Cache=Cache))
if (is.character(Ar@ErrorMessage)) print(Ar@ErrorMessage)
Res=Ar@GetTotalArrayResult
return(as.list(Res))
}
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