Access the raw data from an mzR object.

Description

Access the MS raw data. The peaks and peaksCount functions return the (m/z,intensity) pairs and the number peaks in the spectrum/spectra. peaks returns a single matrix if scans is a numeric of length 1 and a list of matrices if several scans are asked for or no scans argument is provided (i.e all spectra in the oject are retured). peaksCount will return a numeric of length n.

The header function returns a list containing seqNum, acquisitionNum , msLevel, peaksCount, totIonCurrent, retentionTime, basePeakMZ, basePeakIntensity, collisionEnergy, ionisationEnergy, lowM, highMZ, precursorScanNum, precursorMZ, precursorCharge, precursorIntensity, mergedScan, mergedResultScanNum, mergedResultStartScanNum and mergedResultEndScanNum, when available in the original file. If multiple scans are queried, a data.frame is returned with the scans reported along the rows.

The get3Dmap function performs a simple resampling between lowMz and highMz with reMz resolution. A matrix of dimensions length(scans) times seq(lowMz,highMz,resMz) is returned.

Usage

 header(object, scans, ...)

 peaksCount(object, scans, ...)

 peaks(object, ...)

 get3Dmap(object, scans, lowMz, highMz, resMz, ...)

Arguments

Author(s)

Steffen Neumann and Laurent Gatto

See Also

instrumentInfo for metadata access and the "mzR" class.

Examples

 library(msdata)
 filepath <- system.file("microtofq", package = "msdata")
 file <- list.files(filepath, pattern="MM14.mzML",
                     full.names=TRUE, recursive = TRUE)
 mz <- openMSfile(file)
 runInfo(mz)
 colnames(header(mz))
 close(mz)

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(mzR)
Loading required package: Rcpp
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/mzR/peaks.Rd_%03d_medium.png", width=480, height=480)
> ### Name: peaks
> ### Title: Access the raw data from an 'mzR' object.
> ### Aliases: peaks header peaksCount get3Dmap
> 
> ### ** Examples
> 
>  library(msdata)
>  filepath <- system.file("microtofq", package = "msdata")
>  file <- list.files(filepath, pattern="MM14.mzML",
+                      full.names=TRUE, recursive = TRUE)
>  mz <- openMSfile(file)
>  runInfo(mz)
$scanCount
[1] 112

$lowMz
[1] 0

$highMz
[1] 0

$dStartTime
[1] 270.334

$dEndTime
[1] 307.678

$msLevels
[1] 1

>  colnames(header(mz))
 [1] "seqNum"                   "acquisitionNum"          
 [3] "msLevel"                  "polarity"                
 [5] "peaksCount"               "totIonCurrent"           
 [7] "retentionTime"            "basePeakMZ"              
 [9] "basePeakIntensity"        "collisionEnergy"         
[11] "ionisationEnergy"         "lowMZ"                   
[13] "highMZ"                   "precursorScanNum"        
[15] "precursorMZ"              "precursorCharge"         
[17] "precursorIntensity"       "mergedScan"              
[19] "mergedResultScanNum"      "mergedResultStartScanNum"
[21] "mergedResultEndScanNum"  
>  close(mz)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>