msms.dataset: LC-MS/MS dataset

In msmsEDA: Exploratory Data Analysis of LC-MS/MS data by spectral counts

Description

A MSnSet with a spectral counts matrix as expression and two factors in the phenoData.
The spectral counts matrix has samples in the columns, and proteins in the rows.
The factors give the treatment and batch conditions of each sample in the dataset.

Usage

data(msms.dataset)

Format

A MSnSet

References

Josep Gregori, Laura Villarreal, Olga Mendez, Alex Sanchez, Jose Baselga, Josep Villanueva, "Batch effects correction improves the sensitivity of significance tests in spectral counting-based comparative discovery proteomics." J Proteomics. 2012 Jul 16;75(13):3938-51. doi: 10.1016/j.jprot.2012.05.005. Epub 2012 May 12.

Laurent Gatto and Kathryn S. Lilley, MSnbase - an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation, Bioinformatics 28(2), 288-289 (2012).

See Also

See MSnSet for detail on the class, and the exprs and pData accessors.

Examples

data(msms.dataset)
msms.dataset
dim(msms.dataset)
head(exprs(msms.dataset))
head(pData(msms.dataset))
table(pData(msms.dataset)$treat)
table(pData(msms.dataset)$batch)
table(pData(msms.dataset)$treat, pData(msms.dataset)$batch)

Example output

Loading required package: 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, sd, var, xtabs

The following objects are masked from ‘package:base’:

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

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: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: ProtGenerics

Attaching package: ‘ProtGenerics’

The following object is masked from ‘package:stats’:

    smooth


This is MSnbase version 2.16.0 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: ‘MSnbase’

The following object is masked from ‘package:base’:

    trimws

MSnSet (storageMode: lockedEnvironment)
assayData: 697 features, 14 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: U2.2502.1 U2.2502.2 ... U6.0302.3 (14 total)
  varLabels: treat batch
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
  pubMedIds: http://www.ncbi.nlm.nih.gov/pubmed/22588121 
Annotation:  
- - - Processing information - - -
 MSnbase version: 1.8.0 
[1] 697  14
        U2.2502.1 U2.2502.2 U2.2502.3 U2.2502.4 U6.2502.1 U6.2502.2 U6.2502.3
YJR104C       156       176       201       203       194       208       215
YKL060C       183       205       202       171       171       171       149
YDR155C       180       184       198       185       161       160       166
YGR192C       176       172       174       170       170       171       162
YOL086C       171       182       137       103       159       164       116
YLR150W        97       111       104       100        99       103        98
        U6.2502.4 U2.0302.1 U2.0302.2 U2.0302.3 U6.0302.1 U6.0302.2 U6.0302.3
YJR104C       217       246       266       261       249       240       265
YKL060C       144       247       249       236       278       252       247
YDR155C       168       193       175       155       179       165       154
YGR192C       167       243       310       270       270       275       259
YOL086C       113       409       384       364       395       358       355
YLR150W       103        73        90        96        79        81        88
          treat batch
U2.2502.1  U200  2502
U2.2502.2  U200  2502
U2.2502.3  U200  2502
U2.2502.4  U200  2502
U6.2502.1  U600  2502
U6.2502.2  U600  2502

U200 U600 
   7    7 

0302 2502 
   6    8 
      
       0302 2502
  U200    3    4
  U600    3    4

msmsEDA documentation built on Nov. 8, 2020, 6:55 p.m.