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Last data update: 2014.03.03

R: Read an 'mzTab' file

readMzTabData

R Documentation

Read an 'mzTab' file

Description

This function can be used to create an "MSnSet" by reading and parsing an mzTab file. The metadata section is always used to populate the MSnSet's experimentData()@other$mzTab slot.

Usage

readMzTabData(file, what = c("PRT", "PEP", "PSM"), version = c("1.0",
  "0.9"), verbose = TRUE)

Arguments

`file`	A `character` with the `mzTab` file to be read in.
`what`	One of `"PRT"`, `"PEP"` or `"PSM"`, defining which of protein, peptide PSMs section should be returned as an `MSnSet`.
`version`	A `character` defining the format specification version of the mzTab file. Default is `"1.0"`. Version `"0.9"` is available of backwards compatibility. See `readMzTabData_v0.9` for details.
`verbose`	Produce verbose output.

Value

An instance of class MSnSet.

Author(s)

Laurent Gatto

Examples

testfile <- "https://raw.githubusercontent.com/HUPO-PSI/mzTab/master/examples/PRIDE_Exp_Complete_Ac_16649.xml-mztab.txt"
prot <- readMzTabData(testfile, "PRT")
prot
head(fData(prot))
head(exprs(prot))
psms <- readMzTabData(testfile, "PSM")
psms
head(fData(psms))

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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Type 'license()' or 'licence()' for distribution details.

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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/readMzTabData.Rd_%03d_medium.png", width=480, height=480)
> ### Name: readMzTabData
> ### Title: Read an 'mzTab' file
> ### Aliases: readMzTabData
> 
> ### ** Examples
> 
> testfile <- "https://raw.githubusercontent.com/HUPO-PSI/mzTab/master/examples/PRIDE_Exp_Complete_Ac_16649.xml-mztab.txt"
> prot <- readMzTabData(testfile, "PRT")
> prot
MSnSet (storageMode: lockedEnvironment)
assayData: 1249 features, 4 samples 
  element names: exprs 
protocolData: none
phenoData: none
featureData
  featureNames: X223462890 X19855078 ... X26329627 (1249 total)
  fvarLabels: accession description ... protein_coverage (15 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
  pubMedIds: pubmed:21398567 
Annotation:  
- - - Processing information - - -
 MSnbase version: 1.20.7 
> head(fData(prot))
           accession
X223462890 223462890
X19855078   19855078
X21450277   21450277
X6978545     6978545
X51315739   51315739
X117938332 117938332
                                                                                                                                                                                                          description
X223462890                                                                                                                                                                               Spna2 protein [Mus musculus]
X19855078  RecName: Full=Sodium/potassium-transporting ATPase subunit alpha-3; Short=Na(+)/K(+) ATPase alpha-3 subunit; AltName: Full=Na(+)/K(+) ATPase alpha(III) subunit; AltName: Full=Sodium pump subunit alpha-3
X21450277                                                                                                                               sodium/potassium-transporting ATPase subunit alpha-1 precursor [Mus musculus]
X6978545                                                                                                                           sodium/potassium-transporting ATPase subunit alpha-2 precursor [Rattus norvegicus]
X51315739                                                                                                                                                                               RecName: Full=Protein bassoon
X117938332                                                                                                                                                      spectrin beta chain, brain 1 isoform 1 [Mus musculus]
           taxid              species       database database_version
X223462890 10090 Mus musculus (Mouse) NCBInr_2010_10  nr_101020.fasta
X19855078  10090 Mus musculus (Mouse) NCBInr_2010_10  nr_101020.fasta
X21450277  10090 Mus musculus (Mouse) NCBInr_2010_10  nr_101020.fasta
X6978545   10090 Mus musculus (Mouse) NCBInr_2010_10  nr_101020.fasta
X51315739  10090 Mus musculus (Mouse) NCBInr_2010_10  nr_101020.fasta
X117938332 10090 Mus musculus (Mouse) NCBInr_2010_10  nr_101020.fasta
                        search_engine best_search_engine_score.1.
X223462890 [MS, MS:1001207, Mascot, ]                     6539.67
X19855078  [MS, MS:1001207, Mascot, ]                     6331.91
X21450277  [MS, MS:1001207, Mascot, ]                     4577.11
X6978545   [MS, MS:1001207, Mascot, ]                     4342.81
X51315739  [MS, MS:1001207, Mascot, ]                     4177.55
X117938332 [MS, MS:1001207, Mascot, ]                     4001.66
           search_engine_score.1._ms_run.1. num_psms_ms_run.1.
X223462890                          6539.67                157
X19855078                           6331.91                144
X21450277                           4577.11                112
X6978545                            4342.81                108
X51315739                           4177.55                100
X117938332                          4001.66                109
           num_peptides_distinct_ms_run.1. num_peptides_unique_ms_run.1.
X223462890                              92                            NA
X19855078                               49                            NA
X21450277                               39                            NA
X6978545                                42                            NA
X51315739                               59                            NA
X117938332                              72                            NA
           ambiguity_members
X223462890                NA
X19855078                 NA
X21450277                 NA
X6978545                  NA
X51315739                 NA
X117938332                NA
                                                                                modifications
X223462890                                                                               <NA>
X19855078  32-MOD:00425,525-MOD:00425,606-MOD:00425,725-MOD:00425,739-MOD:00425,940-MOD:00425
X21450277                              42-MOD:00425,616-MOD:00425,749-MOD:00425,950-MOD:00425
X6978545                               40-MOD:00425,613-MOD:00425,746-MOD:00425,947-MOD:00425
X51315739                                                                                <NA>
X117938332                                                                               <NA>
           protein_coverage
X223462890                0
X19855078                 0
X21450277                 0
X6978545                  0
X51315739                 0
X117938332                0
> head(exprs(prot))
           protein_abundance_assay.1. protein_abundance_assay.2.
X223462890                          1                      0.853
X19855078                          NA                         NA
X21450277                           1                      0.776
X6978545                            1                      0.784
X51315739                          NA                         NA
X117938332                          1                      0.865
           protein_abundance_assay.3. protein_abundance_assay.4.
X223462890                      0.864                      0.791
X19855078                          NA                         NA
X21450277                       0.819                      0.687
X6978545                        0.848                      0.693
X51315739                          NA                         NA
X117938332                      0.861                      0.795
> psms <- readMzTabData(testfile, "PSM")
> psms
MSnSet (storageMode: lockedEnvironment)
assayData: 8761 features, 0 samples 
  element names: exprs 
protocolData: none
phenoData: none
featureData
  featureNames: X1661 X2280 ... X20346 (8761 total)
  fvarLabels: sequence PSM_ID ... end (18 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
  pubMedIds: pubmed:21398567 
Annotation:  
- - - Processing information - - -
 MSnbase version: 1.20.7 
> head(fData(psms))
      sequence PSM_ID accession unique       database database_version
X1661   QQVLDR   1661 223462890     NA NCBInr_2010_10  nr_101020.fasta
X2280   LVQYLR   2280 223462890     NA NCBInr_2010_10  nr_101020.fasta
X2281   LVQYLR   2281 223462890     NA NCBInr_2010_10  nr_101020.fasta
X2537   LQQLFR   2537 223462890     NA NCBInr_2010_10  nr_101020.fasta
X2809 EAGSVSLR   2809 223462890     NA NCBInr_2010_10  nr_101020.fasta
X5465 LSILSEER   5465 223462890     NA NCBInr_2010_10  nr_101020.fasta
                   search_engine search_engine_score.1. modifications
X1661 [MS, MS:1001207, Mascot, ]                  37.76   0-MOD:01499
X2280 [MS, MS:1001207, Mascot, ]                  44.64   0-MOD:01499
X2281 [MS, MS:1001207, Mascot, ]                  44.76   0-MOD:01499
X2537 [MS, MS:1001207, Mascot, ]                  45.41   0-MOD:01499
X2809 [MS, MS:1001207, Mascot, ]                  55.05   0-MOD:01499
X5465 [MS, MS:1001207, Mascot, ]                  39.82   0-MOD:01499
      retention_time charge exp_mass_to_charge calc_mass_to_charge
X1661             NA      1           902.4821            902.5181
X2280             NA      1           935.5775            935.5800
X2281             NA      1           935.5833            935.5800
X2537             NA      1           948.5956            948.5753
X2809             NA      1           962.5098            962.5393
X5465             NA      1          1090.6232           1090.6230
                  spectra_ref pre post start  end
X1661 ms_run[1]:spectrum=1661   R    Y    20   25
X2280 ms_run[1]:spectrum=2280   K    E   151  156
X2281 ms_run[1]:spectrum=2281   K    E   151  156
X2537 ms_run[1]:spectrum=2537   R    D   786  791
X2809 ms_run[1]:spectrum=2809   K    M  1058 1065
X5465 ms_run[1]:spectrum=5465   K    T   442  449
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>