Create a stratified 'test' MSnSet

Description

This function creates a stratified 'test' MSnSet which can be used for algorihtmic development. A "MSnSet" containing only the marker proteins, as defined in fcol, is returned with a new feature data column appended called test in which a stratified subset of these markers has been relabelled as 'unknowns'.

Usage

testMSnSet(object, fcol = "markers", size = 0.2, seed)

Arguments

Value

An instance of class "MSnSet" which contains only the proteins that have a labelled localisation i.e. the marker proteins, as defined in fcol and a new column in the feature data slot called test which has part of the labels relabelled as "unknown" class (the number of proteins renamed as "unknown" is according to the parameter size).

Author(s)

Lisa Breckels

See Also

sampleMSnSet unknownMSnSet markerMSnSet

Examples

library(pRolocdata)
data(tan2009r1)
sample <- testMSnSet(tan2009r1)
getMarkers(sample, "test")
all(dim(sample) == dim(markerMSnSet(tan2009r1)))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(pRoloc)
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, 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

Loading required package: MLInterfaces
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: XML
Loading required package: cluster

This is pRoloc version 1.12.4 
  Read '?pRoloc' and references therein for information
  about the package and how to get started.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/pRoloc/testMSnSet.Rd_%03d_medium.png", width=480, height=480)
> ### Name: testMSnSet
> ### Title: Create a stratified 'test' 'MSnSet'
> ### Aliases: testMSnSet
> 
> ### ** Examples
> 
> library(pRolocdata)

This is pRolocdata version 1.10.0.
Use 'pRolocdata()' to list available data sets.
> data(tan2009r1)
> sample <- testMSnSet(tan2009r1)
> getMarkers(sample, "test")
organelleMarkers
 Cytoskeleton            ER         Golgi      Lysosome       Nucleus 
            5            22            10             6            16 
           PM    Peroxisome    Proteasome  Ribosome 40S  Ribosome 60S 
           27             3            12            16            25 
mitochondrion       unknown 
           23            46 
> all(dim(sample) == dim(markerMSnSet(tan2009r1)))
[1] TRUE
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>