Last data update: 2014.03.03

 R: Import mgf files as 'MSnExp' instances.
readMgfDataR Documentation

Import mgf files as 'MSnExp' instances.

Description

Reads a mgf file and generates an "MSnExp" object.

Usage

readMgfData(file, pdata = NULL, centroided = TRUE, smoothed = FALSE,
verbose = TRUE, cache = 1)

Arguments

file

character vector with file name to be read.

pdata

an object of class "NAnnotatedDataFrame".

smoothed

Logical indicating whether spectra already smoothed or not. Default is 'FALSE'. Used to initialise "MSnProcess" object in processingData slot.

centroided

Logical indicating whether spectra are centroided or not. Default is 'TRUE'. Used to initialise "MSnProcess" object in processingData slot.

cache

Numeric indicating caching level. Default is 1. Under development.

verbose

verbosity flag.

Details

Note that when reading an mgf file, the original order of the spectra is lost. Thus, if the data was originally written to mgf from an MSnExp object using writeMgfData, although the feature names will be identical, the spectra are not as a result of the reordering. See example below.

Value

An instance of

Author(s)

Guangchuang Yu <guangchuangyu@gmail.com> and Laurent Gatto <lg390@cam.ac.uk>

See Also

writeMgfData method to write the content of "Spectrum" or "MSnExp" objects to mgf files. Raw data files can also be read with the readMSData function.

Examples

  data(itraqdata)
  writeMgfData(itraqdata, con="itraqdata.mgf", COM="MSnbase itraqdata")
  itraqdata2 <- readMgfData("itraqdata.mgf")
  ## note that the order of the spectra is altered
  ## and precision of some values (precursorMz for instance)
  match(signif(precursorMz(itraqdata2),4),signif(precursorMz(itraqdata),4))
  ## [1]  1 10 11 12 13 14 15 16 17 18 ...
  ## ... but all the precursors are there
  all.equal(sort(precursorMz(itraqdata2)),
            sort(precursorMz(itraqdata)),
            check.attributes=FALSE,
            tolerance=10e-5)
  ## is TRUE
  all.equal(as.data.frame(itraqdata2[[1]]),as.data.frame(itraqdata[[1]]))
  ## is TRUE
  all.equal(as.data.frame(itraqdata2[[3]]),as.data.frame(itraqdata[[11]]))
  ## is TRUE
  file <- dir(system.file(package="MSnbase",dir="extdata"),
              full.name=TRUE,
              pattern="test.mgf")
  (x <- readMgfData(file))
  x[[2]]
  precursorMz(x[[2]])
  precursorIntensity(x[[2]])
  precursorMz(x[[1]])
  precursorIntensity(x[[1]]) ## was not in test.mgf
  scanIndex(x)

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(MSnbase)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: mzR
Loading required package: Rcpp
Loading required package: BiocParallel
Loading required package: ProtGenerics

This is MSnbase version 1.20.7 
  Read '?MSnbase' and references therein for information
  about the package and how to get started.


Attaching package: 'MSnbase'

The following object is masked from 'package:stats':

    smooth

The following object is masked from 'package:base':

    trimws

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MSnbase/readMgfData.Rd_%03d_medium.png", width=480, height=480)
> ### Name: readMgfData
> ### Title: Import mgf files as 'MSnExp' instances.
> ### Aliases: readMgfData
> ### Keywords: file
> 
> ### ** Examples
> 
>   data(itraqdata)
>   writeMgfData(itraqdata, con="itraqdata.mgf", COM="MSnbase itraqdata")
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>   itraqdata2 <- readMgfData("itraqdata.mgf")
Scanning itraqdata.mgf ...
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>   ## note that the order of the spectra is altered
>   ## and precision of some values (precursorMz for instance)
>   match(signif(precursorMz(itraqdata2),4),signif(precursorMz(itraqdata),4))
 [1]  1 10 11 12 13 14 15 16 17 18 19  2 20 21 22 23 24 25 26 27 28 29  3 30 31
[26] 32 33 34 35 36 37 38 39  4 40 41 42 43 44 45 46 47 48 49  5 50 51 52 53 54
[51] 55  6  7  8  9
>   ## [1]  1 10 11 12 13 14 15 16 17 18 ...
>   ## ... but all the precursors are there
>   all.equal(sort(precursorMz(itraqdata2)),
+             sort(precursorMz(itraqdata)),
+             check.attributes=FALSE,
+             tolerance=10e-5)
[1] TRUE
>   ## is TRUE
>   all.equal(as.data.frame(itraqdata2[[1]]),as.data.frame(itraqdata[[1]]))
[1] TRUE
>   ## is TRUE
>   all.equal(as.data.frame(itraqdata2[[3]]),as.data.frame(itraqdata[[11]]))
[1] TRUE
>   ## is TRUE
>   file <- dir(system.file(package="MSnbase",dir="extdata"),
+               full.name=TRUE,
+               pattern="test.mgf")
>   (x <- readMgfData(file))
Scanning /home/ddbj/local/lib64/R/library/MSnbase/extdata/test.mgf ...
   |                                                                               |                                                                      |   0%   |                                                                               |=======================                                               |  33%   |                                                                               |===============================================                       |  67%   |                                                                               |======================================================================| 100%
Object of class "MSnExp"
 Object size in memory: 0.04 Mb
- - - Spectra data - - -
 MS level(s): 2 
 Number of MS1 acquisitions: 1 
 Number of MSn scans: 3 
 Number of precursor ions: 3 
 3 unique MZs
 Precursor MZ's: 780.84 - 816.34 
 MSn M/Z range: 101.07 1406.58 
 MSn retention times: 17:8 - 18:47 minutes
- - - Processing information - - -
Data loaded: Wed Jul  6 01:09:59 2016 
 MSnbase version: 1.20.7 
- - - Meta data  - - -
phenoData
  rowNames: 1
  varLabels: sampleNames fileNumbers
  varMetadata: labelDescription
Loaded from:
  test.mgf 
protocolData: none
featureData
  featureNames: X1 X2 X3
  fvarLabels: TITLE PEPMASS ... SCANS (5 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
>   x[[2]]
Object of class "Spectrum2"
 Precursor: 787.8283 
 Retention time: 18:37 
 Charge: 2 
 MSn level: 2 
 Peaks count: 21 
 Total ion count: 124558.3 
>   precursorMz(x[[2]])
PEPMASSMZ 
 787.8283 
>   precursorIntensity(x[[2]])
PEPMASSINT 
  880650.4 
>   precursorMz(x[[1]])
PEPMASSMZ 
 816.3383 
>   precursorIntensity(x[[1]]) ## was not in test.mgf
PEPMASSINT 
         0 
>   scanIndex(x)
  X1   X2   X3 
2162 2406 2432 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>


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