Read an 'mzTab' file

Description

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

Usage

readMzTabData_v0.9(file, what = c("PRT", "PEP"), verbose = TRUE)

Arguments

Value

An instance of class MSnSet.

Author(s)

Laurent Gatto

See Also

writeMzTabData to save an "MSnSet" as an mzTab file.

Examples

testfile <- "https://raw.githubusercontent.com/HUPO-PSI/mzTab/master/legacy/jmztab-1.0/examples/mztab_itraq_example.txt"
prot <- readMzTabData_v0.9(testfile, "PRT")
prot
pep <- readMzTabData_v0.9(testfile, "PEP")
pep

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 '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.
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> 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_v0.9.Rd_%03d_medium.png", width=480, height=480)
> ### Name: readMzTabData_v0.9
> ### Title: Read an 'mzTab' file
> ### Aliases: readMzTabData_v0.9
> 
> ### ** Examples
> 
> testfile <- "https://raw.githubusercontent.com/HUPO-PSI/mzTab/master/legacy/jmztab-1.0/examples/mztab_itraq_example.txt"
> prot <- readMzTabData_v0.9(testfile, "PRT")
Version 0.9 is deprecated. Please see '?readMzTabData' and '?MzTab' for details.
Detected a metadata section
Detected a protein section
> prot
MSnSet (storageMode: lockedEnvironment)
assayData: 2 features, 4 samples 
  element names: exprs 
protocolData: none
phenoData
  rowNames: sub[1] sub[2] sub[3] sub[4]
  varLabels: abundance
  varMetadata: labelDescription
featureData
  featureNames: 1 2
  fvarLabels: accession unit_id ... protein_abundance_std_error_sub[4]
    (26 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  
- - - Processing information - - -
mzTab read: Wed Jul  6 01:10:18 2016 
 MSnbase version: 1.20.7 
> pep <- readMzTabData_v0.9(testfile, "PEP")
Version 0.9 is deprecated. Please see '?readMzTabData' and '?MzTab' for details.
Detected a metadata section
Detected a peptide section
> pep
MSnSet (storageMode: lockedEnvironment)
assayData: 6 features, 4 samples 
  element names: exprs 
protocolData: none
phenoData
  rowNames: sub[1] sub[2] sub[3] sub[4]
  varLabels: abundance
  varMetadata: labelDescription
featureData
  featureNames: 1 2 ... 6 (6 total)
  fvarLabels: sequence accession ... peptide_abundance_std_error_sub[4]
    (23 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  
- - - Processing information - - -
mzTab read: Wed Jul  6 01:10:18 2016 
 MSnbase version: 1.20.7 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>